Carditamera bajaensis, new species, is described from semi-infaunal specimens collected in the intertidal zone in the Golfo de California, Baja California Sur, Mexico. The new species resembles Carditamera affinis (G. B. Sowerby I, 1833), the only valid Carditamera species known from within the Golfo de California, with which it has been mistaken, but it differs in shell structure and most conspicuously in life mode — semi-infaunal for C. bajaensis versus byssally attached to hard substrata for C. affinis. Haplotype networks constructed from two mitochondrial genes (16S rRNA and cytochrome b) and one nuclear gene (internal transcribed spacer 2) indicate a clear genetic break between C. affinis and C. bajaensis, as suspected initially due to their different modes of life and shell morphology. This pair of species, C. affinis and C. bajaensis, overlapping in distribution yet genetically distinct, possibly indicate ecological speciation.