Giant clams are widely depleted with the exception of French Polynesia, where the dominant species, Tridacna maxima, is still exploited. Here, we report the first genetic structure analysis of T. maxima samples, issued from 4 polynesian archipelagos and spread on a surface of about 4 millions square kilometers. This study was based on both mitochondrial (COI and 16S) and nuclear (18S) sequences and led to the discovery of two new T. maxima clades, which diverged 1.5 millions of years before present. French Polynesian clades cohabite over a large area with a North-West South-East axis on either side of which, one of each clade is dominant. Contrary to the strong genetic structuration observed in the T. maxima population in Indo- and West Pacific, we show here that the populations are widely interconnected, except in Tuamotu archipelago. This is underlined by a high connectivity between distant islands and archipelagos, which is independent from the direction of the oceanic currents. Altogether our data bring growing evidences of a progression of both clades in French Polynesia, one south and one north.