||Long-term prey population histories are fundamental to reconstructing spatial and temporal variation in human diet, hunting technology, capture strategies, and a host of other prehistoric hunting behaviors. Typically, such reconstructions have involved the use of taxonomic relative abundance indexes from bone counts as measures of population history, but such measures are subject to many complicating quantitative and taphonomic issues. Fortunately, animal populations maintain a record of population history in the form of genetic diversity. By assessing temporal variation in the genetic diversity of populations, zooarchaeologists have access to this history. This dissertation describes research that was designed to use the genetic record of population history to develop long-term histories of two prey species and to compare these genetic diversity-derived histories with those drawn from relative abundance measures. Taxonomic relative abundance measures from California's San Miguel Island suggest that Guadalupe fur seals maintained a large and stable population through the late Holocene, whereas the archaeological record of Tule elk in California's San Francisco Bay area suggests a late Holocene population bottleneck. To evaluate the genetic diversity implications of these two contexts, I obtained ancient DNA sequences from 39 Guadalupe fur seal specimens from four archaeological sites on San Miguel Island and from 24 Tule elk specimens from the San Francisco Bay area's Emeryville Shellmound. In both cases trends in genetic diversity support inferences made from relative abundance data. Guadalupe fur seal sequences, aggregated into three late Holocene temporal periods, show considerable genetic diversity within each period and no differentiation between periods suggesting a large and stable population. Tule elk sequences were divided into two groups that span a hypothesized population bottleneck. Analysis of these aggregations shows considerable diversity among pre-bottleneck sequences but no diversity in post-bottleneck sequences. This result is surprising for Guadalupe fur seals whose life history characteristics suggest that their populations are rather susceptible to hunting pressure. One plausible reason for long-term stability of Guadalupe fur seal populations in the face of what was likely significant hunting pressure is the presence of population refugia from which migration sustained genetically diverse populations.