Late Quaternary histories of two North American desert biomes—C4 grasslands and C3 shrublands—are poorly known despite their sensitivity and potential value in reconstructing summer rains and winter temperatures. Plant macrofossil assemblages from packrat midden series in the northern Chihuahuan Desert show that C4 grasses and annuals typical of desert grassland persisted near their present northern limits throughout the last glacial-interglacial cycle. By contrast, key C3 desert shrubs appeared somewhat abruptly after 5000cal.yrBP. Bioclimatic envelopes for select C4 and C3 species are mapped to interpret the glacial-interglacial persistence of desert grassland and the mid-to-late Holocene expansion of desert shrublands. The envelopes suggest relatively warm Pleistocene temperatures with moist summers allowed for persistence of C4 grasses, whereas winters were probably too cold (or too wet) for C3 desert shrubs. Contrary to climate model results, core processes associated with the North American Monsoon and moisture transport to the northern Chihuahuan Desert remained intact throughout the last glacial-interglacial cycle. Mid-latitude effects, however, truncated midsummer (July-August) moisture transport north of 35° N. The sudden expansion of desert shrublands after 5000cal.yrBP may be a threshold response to warmer winters associated with increasing boreal winter insolation, and enhanced El Niño-Southern Oscillation variability.