Aneuploidy is a cytogenetic phenomenon known as an abnormal diploid chromosome number. A negative relationship between growth rate, one of the biggest problems faced by bivalve producers, and this phenomenon was already verified for two oyster species, the Japanese oyster Crassostrea gigas, the Portuguese oyster Crassostrea angulata and their interspecific hybrids and, more recently, in the carpet shell clam Ruditapes decussatus. The main objective of this study was to assess whether chromosome losses in aneuploid situations could be explained by differential chromosomal susceptibility, as previously reported in the oyster C. gigas. Thereby, we applied the restriction enzyme (RE) digestion chromosome banding technique to aneuploid karyotypes of R. decussatus and C. angulata, in order to identify the missing chromosomes. The results of this study showed that 4 out of the 19 chromosome pairs (viz. 1, 6, 12, and 19) of R. decussatus and 3 out of the 10 chromosome pairs (viz. 1, 9, and 10) of C. angulata were preferentially affected by the loss of one homologous chromosome. The chromosomal loss in C. angulata was very similar to the one previously observed in C. gigas. These results open a new field for further research in order to have a better understanding of the aneuploidy phenomenon in bivalves and particularly its negative relationship with growth rate.