A new species of giant clam from northern Australian coastal waters is distinguished principally on genetic evidence. Of Recent tridacnids, Tridacna ningaloo n. sp. is morphologically closest to the most widespread species in the Indo-Pacific, Tridacna maxima (Röding, 1798), yet genetically closest to the species pair T. squamosa Lamarck, 1819 plus T. crocea Lamarck, 1819. Genotype data are provided for the type material of T. ningaloo n. sp. The greatest significance of this new, cryptic species is that it casts doubt on the correctness of the ‘historical’ giant clam species defined solely on conchological characters, particularly T. maxima. This paper supports the retention of all giant clams in the family Tridacnidae, as distinct from the Cardiidae, because of their numerous morphological apomorphies, specialised ecological niche, and independent acquisition of symbiotic zooxanthellae.