Aneuploidy, or presence of an abnormal number of chromosomes, has been commonly observed in marine bivalves. This phenomenon has also been shown to be negatively correlated with growth and survival rates in several species of oysters and clams. The impact of pollutants on the aneuploidy level in bivalves has also been previously demonstrated. Over the past two decades, evidence of nonrandom chromosomal loss has been demonstrated, with the identification of the missing chromosomes in aneuploid karyotypes reported in several species. The results have shown that only a few pairs were preferentially affected by the loss of one homologue chromosome in different species of oysters and clams. Recently, during the genotoxicity assessment of the marine environment in Qatar using the pearl oyster Pinctada radiata (Leach, 1814) as model and surrogate species, we observed hypodiploid and hyperdiploid karyotypes. Hyperdiploidy was more frequent, which is highly uncommon in bivalves. The identification of the extra and missing chromosomes in aneuploid cells showed that pairs 4, 5, 12, and 13 were found to be more susceptible than others in having an extra individual chromosome. The same set of pairs showed a tendency to lose one homologue chromosome. Several hypotheses on the preferential chromosomal susceptibility in bivalves, in general, are discussed.