The opinion of the court was delivered by: Colleen Kollar-kotelly United States District Judge
Plaintiff, WildEarth Guardians, brings this action against Defendant, Ken Salazar, Secretary of the Interior,*fn1 pursuant to the Administrative Procedure Act ("APA"). 5 U.S.C. § 701 et. seq. Plaintiff seeks judicial review of the Fish and Wildlife Service's ("FWS") final agency actions denying Plaintiff's petition to reclassify the Utah prairie dog as an endangered species under the Endangered Species Act ("ESA"), 16 U.S.C. § 1531 et. seq., as well as Plaintiff's petition to initiate rulemaking to repeal a regulation allowing for the limited extermination of Utah prairie dogs. Currently before the Court are Plaintiff's  Motion for Summary Judgment ("Pl.'s Mot."), Defendant's  Cross-Motion for Summary Judgment ("Def.'s Cross-Mot."), and Plaintiff's  Reply in Support of Plaintiff's Motion for Summary Judgment ("Pl.'s Reply"). The Court has thoroughly reviewed the parties' submissions, the administrative record, applicable case law, the relevant statutory and regulatory authority, as well as the record of the case as a whole. For the reasons set forth below, the Court shall GRANT-IN-PART and DENY- IN-PART Plaintiff's  Motion for Summary Judgment, shall GRANT-IN-PART and DENY-IN-PART Defendant's  Cross-Motion for Summary Judgment, and shall remand this matter to the agency for further consideration consistent with this Memorandum Opinion. Specifically, the Court shall GRANT Plaintiff's Motion for Summary Judgment and DENY Defendant's Cross-Motion for Summary Judgment with respect to Plaintiff's petition to reclassify the Utah prairie dog because (1) FWS failed to explain why the reduction in the species' historical range did not indicate that reclassification may be warranted and (2) FWS failed to consider the cumulative effect of the ESA's listing factors as required under 50 C.F.R. § 424.11(c). In addition, the Court shall DENY Plaintiff's Motion for Summary Judgment and GRANT Defendant's Cross-Motion for Summary Judgment insofar as Plaintiff asserts that FWS' refusal to initiate rulemaking was arbitrary, capricious, and not in accordance with the ESA.
A. Statutory and Regulatory Background
Congress enacted the ESA in 1973 "to provide a means whereby the ecosystems upon which endangered species and threatened species depend may be conserved, [and] to provide a program for the conservation of such endangered and threatened species." 16 U.S.C. § 1531(b). An endangered species is "any species which is in danger of extinction throughout all or a significant portion of its range . . . ." Id. §1532(6). In contrast, a threatened species is one that "is likely to become an endangered species within the foreseeable future . . . ." Id. § 1532(20).
To be protected under the ESA, a species must be "listed" as either an endangered or threatened species by the Secretary of the Interior.*fn2 See id. § 1531(b). Although the Secretary may list species himself, see id. § 1533(a),individual citizens may also petition the Secretary to list, delist, or reclassify a species, see id. § 1533(b)(3)(A). To the extent possible, within 90-days of receiving such a petition, "the Secretary shall make a finding as to whether the petition presents substantial scientific or commercial information indicating that the petitioned action may be warranted." Id.; see also 50 C.F.R. § 424.14(b)(1) (providing that, "to the maximum extent possible," the Secretary is to make this finding within 90-days).
A petition contains "substantial information" when it has an "amount of information that would lead a reasonable person to believe that the measure proposed in the petition may be warranted." Id.*fn3 When determining whether the petitioned action "may be warranted," the Secretary examines the following five listing factors' individual and cumulative effect on the species:
(A) the present or threatened destruction, modification, or curtailment of its habitat or range;
(B) overutilization for commercial, recreational, scientific, or educational purposes;
(C) disease or predation;
(D) the inadequacy of existing regulatory mechanisms; or
(E) other natural or manmade factors affecting its continued existence.
16 U.S.C. § 1533(a)(1); see also 50 C.F.R. § 424.11(c) (providing that species are to be listed based on "any one or a combination" of the above-mentioned factors). In making this determination, the Secretary may only consider "the best available scientific and commercial information regarding a species' status, without reference to possible economic or other impacts of such determination." Id. § 424.11(b); 16 U.S.C. § 1533(b)(1)(A). The Secretary's finding in regards to a petition, referred to as a "90-day finding," is published in the Federal Register. See id. § 1533(b)(3)(A).
If the Secretary's 90-day finding concludes that the petition presents substantial information in support of the petitioned action, the Secretary then must "promptly commence a review of the status of the species concerned." Id. This review culminates in another finding issued within 12-months of receipt of the petition that concludes whether the petitioned action is:
(a) warranted; (b) not warranted; or (c) warranted but precluded by other listing activity. Id. § 1533(b)(3)(B).
The ESA extends certain protections to listed species, including, most pertinent to this case, a prohibition on the "take" of an endangered species. Id. § 1538(a)(1)(B). The term "take" is defined as "to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to engage in any such conduct." Id. § 1532(19). Although the ESA does not automatically extend the take prohibition to threatened species, the Secretary has the discretion, under ESA subsection 4(d), to "issue such regulations as he deems necessary and advisable to provide for the conservation of [threatened] species." Id. § 1533(d). The Secretary has exercised this discretion to generally extend the take prohibition to threatened species. See 50 C.F.R. § 17.31.
B. Factual Background*fn4
The Utah prairie dog (Cynomys parvidens) is one of five prairie dogs species, all of which are native to North America and have non-overlapping geographic ranges. AR 1 at 263 (72 Fed. Reg. 7843, 7843 (Feb. 21, 2007) (FWS' 90-day finding) (hereinafter "Finding")).*fn5 The Utah prairie dog's range is confined to five southwestern Utah counties, rendering it currently the most geographically restricted of all prairie dog species. Id. at 263-64. The Utah prairie dog lives in aggregations called colonies, towns, or villages. Id. at 903 (John L. Hoogland, Black-tailed Prairie Dog in Wild Mammals of North America: Biology, Management, and Conservation 232, 237 (George A. Feldhamer, Bruce C. Thompson & Joseph A. Chapman eds., 2nd ed. 2003)). Its preferred habitat consists of swale formations with moist herbage and well-drained soil conducive for burrowing. Id. at 264 (Finding). Utah prairie dogs are also predominately herbivores, preferring alfalfa and grasses, and are true hibernators that cease most surface activity during the harsher winter months. Id.
Although the first Utah prairie dog census was not conducted until 1976, historical estimates have placed the species' population in the 1920s at 95,000 animals across a range of 713 square miles.*fn6 Id. Since then, the species has declined due to drought, habitat alteration, disease (predominately sylvatic plague, known as bubonic plague in humans), and targeted eradication by humans. See id. at 264, 268; id. at 1104 (Rodney L. Player & Philip J. Urness, Habitat Manipulation for Reestablishment of Utah Prairie Dog in Capitol Reef National Park, 42 Great Basin Naturalist 517, 517 (1982)).
In 1973, the species declined to approximately 3300 animals across thirty-seven colonies and, consequently, FWS listed the Utah prairie dog as an endangered species under the ESA. Complaint ¶ 26, Docket No. ; Answer ¶ 26, Docket No. ; see also AR 1 at 251 (38 Fed. Reg. 14678 (June 4, 1973)). Six years later, in 1979, the Utah Division of Wildlife and Resources ("UDWR") petitioned FWS to remove the species from the List of Endangered and Threatened Wildlife. AR 1 at 265 (Finding). In 1984, FWS responded to UDWR's petition by reclassifying the species as threatened and concluded that although "the Utah prairie dog is still threatened over much of its range," because the species' population has increased since 1972, it is not longer in danger of extinction. Id. at 252 (49 Fed. Reg. 22,330, 22330 (May 29, 1984)).
The 1984 reclassification decision was accompanied by a rule promulgated under ESA subsection 4(d) that abrogated the general prohibition on the take of threatened species in regards to the Utah prairie dog and permitted a maximum take of 5000 animals per year under a permitting scheme administered by UDWR. Id. at 252, 255. In 1991, FWS, citing increased population counts, increased the allowed take for Utah prairie dogs to 6000 animals per year (hereinafter "1991 Rule"). AR 1 at 257, 259 (56 Fed. Reg. 27,438, 27,440 (June 14, 1991)). When the pending motions were filed, the 1991 Rule was still in effect. See Pl.'s Reply at 21-22. Under the 1991 Rule, the UDWR issues take permits on a case-by-case basis after considering whether the proposed take "is necessary for the conservation and management of the species and the effect on overall population status." AR 1 at 255 (49 Fed. Reg. at 22,333). Permits are granted only for those Utah prairie dogs causing damage to the land, id. at 259 (56 Fed. Reg. at 27,440), and for no more than ten percent of the animals in a given colony, id. at 269 (72 Fed. Reg. at 7849). From the inception of ...