Assortative mating and reduced hybrid fitness are typically invoked to explain the stability of hybrid zones and the specification of two closely related taxa. Such examples of mate preferences in nature, especially for broadcast free-spawning marine invertebrates, and the understanding of the underlying mechanisms responsible for this positive selection are still lacking. This study documents another example of assortative fertilization by genome in situ hybridization in reciprocal crosses of scallops Chlamys farreri and Patinopecten yessoensis. Females produced eggs selected sperm nonrandomly but showed significant gamete preference of conspecifics over heterospecifics, with Chlamys farrei females using average 89.1% of conspecific sperms and the Patinopecten yessoensis using average 94.3% in natural spawning conditions (temperature 17°C, salinity 31.5‰). This conspecific gamete advantage may be related to the coordinated communication between interacting gametes, and the conspecific bindin genotype selection during the communicational process may also be involved. Two environmental factors, temperature and salinity were also tested to determinate to what extent they affect the patterns of assortative fertilization between these two species. The result showed that temperature seemed to have more influence on assortative fertilization than salinity did. At the temperatures of 11°C, 17°C, 22°C and 26°C, the average conspecific sperms preference of Chlamys farreri eggs was 80.0%, 89.1%, 95.1% and 95.5% respectively, whereas at the salinity of 24‰, 28‰, 31.5‰ and 35.5‰, the average mating preference was 97.2%, 91.2%, 89.1% and 99.5% respectively. These results may have some bearings on the condition dependent alteration in the inter gamete recognition system. Alternatively, it may be simply the byproduct of different sperm tolerance ability under different conditions. The implication it may provide to hybrid production was also discussed.