Aquatic germplasm repositories can play a pivotal role in securing the genetic diversity of natural populations and agriculturally important aquatic species. However, existing technologies for repository development and operation face challenges in terms of accuracy, precision, efficiency, and cost-effectiveness, especially for microdevices used in gamete quality evaluation. Quality management is critical throughout genetic resource protection processes from sample collection to final usage. In this study, we examined the potential of using three-dimensional (3-D) stereolithography resin printing to address these challenges and evaluated the overall capabilities and limitations of a representative industrial 3-D resin printer with a price of US$18,000, a consumer-level printer with a price <US$700, and soft lithography, a conventional microfabrication method. A standardized test object, the Integrated Geometry Sampler (IGS), and a device with application in repository quality management, the Single-piece Sperm Counting Chamber (SSCC), were printed to determine capabilities and evaluate differences in targeted versus printed depths and heights. The IGS design had an array of negative and positive features with dimensions ranging from 1 mm to 0.02 mm in width and depth. The SSCC consisted of grid and wall features to facilitate cell counting. The SSCC was evaluated with polydimethylsiloxane (PDMS) devices cast from a typical photoresist and silicon mold. Fabrication quality was evaluated by optical profilometry for parameters such as dimensional accuracy, precision, and visual morphology. Fabrication time and cost were also evaluated. The precision, reliability, and surface quality of industrial-grade 3-D resin printing were satisfactory for operations requiring depths or heights larger than 0.1 mm due to a low discrepancy between targeted and measured dimensions across a range of 1 mm to 0.1 mm. Meanwhile, consumer-grade printers were suitable for microdevices with depths or heights larger than 0.2 mm. While the performance of either of these printers could be further optimized, their current capabilities, broad availability, low cost of operation, high throughput, and simplicity offer great promise for rapid development and widespread use of standardized microdevices for numerous applications, including gamete quality evaluation and “laboratory-on-a-chip” applications in support of aquatic germplasm repositories.