The geographically widespread mayfly genus Baetis occurs from the subarctic to tropical regions of the world. Many of the 20 described Baetis species in North America are known to show cryptic species diversity. However, studies of Baetis that have examined morphology and genetic diversity have found mixed results in terms of cryptic species, with some studies indicating a complex of related species and others suggesting a single widespread species. We used Bayesian analyses, intra- and interspecific genetic diversity values, and median-joining haplotype networks to compare cytochrome oxidase I (COI) sequences from Baetis specimens from parts of northern and southern California (n = 742). Our results suggest that genetic diversity at the COI gene region in populations from northern California supports the diversity indicated by morphology (Baetis tricaudatus and Baetis adonis); however, populations in southern California exhibit more genetic diversity than indicated by morphology alone (DNA divergence > 1%), which suggests cryptic species diversity. The putative species that was morphologically and genetically identified as Baetis tricaudatus was the only taxon that occurred in both regions. No haplotypes were shared between regions. Intraspecific diversity within putative species from northern California was >1%. In contrast, intraspecific diversity within species from southern California was always <1%. Such discrepancies highlight the need for locally derived reference libraries in using next-generation sequencing or environmental DNA as a method to examine genetic diversity.