This analysis of faunal remains from eleven archaeological sites in the northern San Juan region, extensively occupied by the Ancestral Pueblo people until they leave the region by AD 1300, explores the effects of resource intensification of small wild and domestic resources leading up to this regional depopulation. By examining multiple lines of evidence, in addition to faunal abundance, causal factors are identified to address changes in abundances through time. In particular, age- and sex-based mortality are examined for lagomorphs (jackrabbits and cottontails) and domesticated turkey, respectively, to test hypotheses generated using the prey and patch choice models. Analyses of these resources follow a systematic paleontology which provides explicit identifications made of five sites from a large study area, Goodman Point Pueblo Unit. These data are integrated with those from large village sites from the encompassing central Mesa Verde region. The results of both analyses help clarify why the Ancestral Pueblo people left southwestern Colorado. During the final twenty-year occupation period, the results of this study support a shift from reliance on turkey husbandry to intense exploitation of locally available garden resources (i.e. cottontails).