The Cortes geoduck (Panopea globosa) has been considered a Gulf of California (GC) endemic but anecdotal and unpublished evidence has suggested its presence in Bahía Magdalena (BM), on the Pacific coast of southern Baja California. Establishing the identity of geoduck clams and their distribution limits is not only of clear biological significance to understand their structural and functional variation, but is also of consequence for their conservation and management, given the multi-million dollar fishery they support in north-west Mexico. We analysed Panopea clams from Mexican populations, including BM, using an integrative approach including genetics, morphometrics, and an ecological niche model. Our genetic results (restriction fragment length polymorphisms of nuclear ribosomal DNA and mtDNA cytochrome c oxidase subunit I sequences) clearly identify BM geoducks as P. globosa, implying a significant geographical range expansion outside of the GC and refuting its status as endemic to the Gulf. On the other hand, clams from BM were phenotypically different (shell significantly higher) from other Mexican P. globosa and Panopea generosa specimens, which may account for the confusion in their morphological identification. The ecological niche model for P. globosa, integrating ecological and distributional data from the GC, revealed a very low probability (<10%) that this species could successfully occupy BM. Our results and those of others suggest that the Cortes geoduck population in BM may be adapted to specific environmental conditions differing from those experienced by conspecifics inside the Gulf and is likely isolated. This is highly relevant for the management plans of Mexican geoducks.