© 2016 The Malacological Society of Australasia and the Society for the Study of Molluscan Diversity.Correct identification of species is fundamentally important, but field identification can be misleading in many taxa, requiring genetic comparisons to confirm identity of specimens. Recent genetic studies revealed that the giant clam Tridacna noae (Röding, 1798), previously confused morphologically with Tridacna maxima (Röding, 1798), is widespread in the Indo-West Pacific, including a subtidal site at Ningaloo Reef, Western Australia. We examined molecular and morphological variation of Tridacna from four intertidal populations at Ningaloo Reef to determine their identity and to test whether morphology is useful for distinguishing the two species in this region. DNA sequences of clams identified all individuals as T. noae, indicating that T. maxima is rare, if it occurs at all, at Ningaloo Reef. Morphological traits that distinguish the two species in the Western Pacific are highly variable at Ningaloo, indicating the need for local genetic corroboration for correct identification.