Abstract Objective To support the declining wild population of Delta Smelt, a conservation hatchery has expanded its mission from maintaining a backup population as insurance against extinction to also producing fish for release into the wild. The substantially higher production demands require a balance between producing large numbers of fish while adhering to conservation genetic principles that maximize retention of effective population size (Ne) and thus overall diversity. Methods We performed spawning experiments at the hatchery to evaluate the genetic consequences of two spawning strategies: (1) a pooled strategy where we fertilized premixed eggs from three dams with premixed milt from three sires and (2) a partial-factorial strategy where eggs from three dams were mixed and then apportioned among three containers, each container then receiving milt from one sire. We used genetic parentage analysis of larval offspring to determine the reproductive success of spawners in 10 replicate crosses of each strategy. Result The contributions of parents to offspring were more even in partial-factorial crosses and consequently resulted in higher Ne (average Ne = 5.50 ± 0.38; expected Ne = 6.0), suggesting its potential for maintaining genetic diversity over time. In contrast, our pooled spawning experiment produced lower and more variable Ne values (average Ne = 3.86 ± 1.30), demonstrating that this more efficient method of production entails high costs in terms of long-term genetic management. Treating our experiments as hypothetical pools of fish for release, we combined the Ne values for pooled or partial-factorial crosses to calculate the effective size of a release population (NeR). Unequal family sizes reduced NeR for our pooled experiment to half of the expected value, whereas the partial-factorial experiment NeR was 88% of the expected value. Conclusion We discuss the benefits and risks of each method and how these can be considered when designing a spawning strategy for Delta Smelt supplementation.