Thirty packrat (Neotoma spp.) middens collected from boulder fields near Cataviña, Baja California, Mexico, at 640–680 m elevation provide the first long chronology of macrofossils and pollen spanning the late Quaternary in the Central Desert of Baja California. Midden plant macrofossil and pollen assemblages document a rich chaparral/woodland assemblage during the last glacial and early Holocene dominated by Parry pinyon (Pinus quadrifolia) and California juniper (Juniperus californica) until 11,630 cal yr BP. This indicates chaparral/woodland had a much more extensive distribution in what are now desert elevations in northern and central Baja California. In contrast to late glacial and early Holocene midden records from northeastern Baja, the Cataviña middens of the same age lack plants adapted to warm season precipitation, suggesting that decreased temperatures and evapotranspiration during the growing season and enhanced winter precipitation, with little contribution from summer rains, supported the lowering of chaparral/woodland species distributions in central Baja California. Cataviña middens also record endemic desert plant taxa mixed in with chaparral/woodland species during the Pleistocene, persisting throughout the Holocene, followed by the quick arrival of other desert species after ∼11,000 cal yr BP. Baja California remains a high-potential yet poorly sampled area for packrat midden research in North America.