Most previous studies identifying Panopea generosa and P. globose have used non-rigorous visual methods as well as older shell measurement techniques. Newer mathematical methods based on shell shape variation allow for more accurate identification of clam species, as well as modeling of phenotypic differences due to environmental effects in populations in different sites. Interspecific shell morphology for two Mexican geoduck clam species was analyzed from a total of five sites off both coasts of the Baja California peninsula. In addition, intraspecific analyses of shell morphology were conducted for one of the species, P. globosa, at four sites along its reported distribution. Two approaches were employed for the analyses: a novel approach based on radiating lines to characterize shell outlines, and a more traditional approach using internal shell landmarks. In general, the novel approach afforded greater fidelity in distinguishing inter- and intraspecific variation. Our results from both methods agree with original species descriptions, and showed that Bahía Magdalena geoducks are P. globosa, thus revealing a wider distribution than previous reports for this species. The outline and internal scars were highly discriminant between the two species. Shell shape of P. generosa was also less variable than that of P. globosa. Intraspecific analyses of P. globosa shell shape suggest an adaptive or phenotypic response to environmental conditions at each site. Our results may also be indicative of reproductive isolation between Pacific P. globosa at Bahía Magdalena and conspecifics in the Gulf of California.