The goal was to develop a cost‐effective and portable freezing system for germplasm cryopreservation of fish and shellfish. The objectives were to: (1) identify components for construction of a portable freezing system by evaluating the affecting factors of cooling rates; (2) generate a range of cooling rates through adjusting different variables; (3) compare cooling profiles generated by the aeration freezing system and a commercial programmable freezer, and (4) verify the effectiveness of the aeration freezing system by cryopreserving sperm of eastern oysters Crassostrea virginica. An aeration freezing system was constructed using a Styrofoam box as cooling chamber and an innovative aeration unit to create nitrogen vapour. A wide range of cooling rates (1.5–32.1°C/min) were achieved by combinations of sample position at 2, 5, or 10 cm above liquid nitrogen surface, the temperature of nitrogen vapour (−150 or −180°C), and aeration time of liquid nitrogen (0, 1, 2 min, or continuity). Compared to a programmable freezer, the aeration freezing system generated cooling profiles with significantly higher temperature for ice nucleation initiation. No difference in post‐thaw sperm motility of eastern oysters were found between samples cooling in the aeration freezing system or a programmable freezer. Cooling rates of 10 or 15°C/min from 4°C to −80°C yielded the highest post‐thaw sperm motility regardless of the cooling devices. The aeration freezing system developed in this study has the potential for high‐throughput sample processing, and the design allows easy construction by multiple users. [ABSTRACT FROM AUTHOR]