The Portuguese (Crassostrea angulata) and Pacific oyster (Crassostrea gigas), both from the genus Crassostrea, are two important species for production and conservation. Although they have common characteristics, different susceptibilities to rearing conditions have been described in these species. Overall, in the case of C. angulata, only a few remaining populations are present in the south of Portugal and Spain. The preservation of genetic material from improved stocks or from the original population is crucial in oysters to prevent the potential impacts of epidemic diseases and natural disasters. Sperm cryopreservation in oysters has progressed in recent years. However many issues, such as protocol standardization, are still unsolved for the application of research results. In the present study a sperm cryopreservation protocol, previously published in C. angulata by our group, were analyzed in terms of cellular and molecular damage, in an effort to determine the most sensible parameters to standardize the cryopreservation protocols for both species. Different approaches in the analysis of sperm quality were performed for the first time in this genus to detect different susceptibilities between the two valuable species. Our results revealed that our previously published protocol containing 10% DMSO as cryoprotectant is more suitable comparing to 10% EG in both species. In addition, an integrative analysis was performed in both oyster species comparing all cellular parameters and C. gigas showed a higher susceptibility to cryopreservation using this optimized protocol. Moreover, higher susceptibility to transcript degradation was detected in C. gigas using this optimized cryopreservation protocol. This study highlights the importance of using different techniques and exhaustive analyses for selecting the most suitable cryopreservation protocol and its standardization, thus ensuring the total safety of the technique.