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Arroyos form distinctive habitats in desert foothhills. To document herpetofaunal habitat associations with arroyos we operated 16 drift fences (eight in arroyos, eight on uplands) for 4,152 drift fence nights during spring and fall, 1993-1994. Only Scaphiopus couchii demonstrated an association for arroyo habitat, and only during fall 1993. Cnemidophorzus mannoratus and C. exsanquis demonstrated possible seasonal associations with uplands. Statistical tests are characterized by low power, apparently resulting from small observed differences in relative abundance between habitats. Small observed differences suggest that, with some exceptions, arroyos versus uplands is not a habitat contrast of relevance to herpetofauna. A posteriori canonical correspondence analysis was applied to produce an ordination of species with six structural habitat variables (shrub cover, grass and forb cover at two heights, amount of detritus, stones and rocks, and sand on the substrate). This comparison, although suggesting a tendency for herpetofauna to favor arroyos, failed to show a significant relationship between herpetofauna and environmental variables. This study suggests that environmental variables other than those directly related to vegetation will be important determinants of herpetofaunal habitat suitability.