Hybrid male sterility is frequently observed in the wild between two mouse subspecies – Mus musculus musculus and M. musculus domesticus. This complex trait drives reproductive isolation and ultimately speciation. We have replicated hybrid male sterility in the lab by crossing an inbred mouse strain representing musculus, PWK/PhJ, to four strains that are largely descended from domesticus (Dom). Hybrid males with PWK mothers exhibit a wide spectrum of abnormal reproductive phenotypic variation including reduced testes weights and azoospermia. Importantly, the reciprocal hybrids are reproductively normal and serve as experimental controls in this breeding scheme. We characterized reproductive phenotypes across a panel of 10 genetically distinct hybrid males at 8 weeks of age. PWKxDom hybrid males exhibit significantly lower testis weight and sperm density than reciprocal hybrids. Additionally, we observe significant differences that are driven by the genetic background of each specific hybrid. For example, PWKxA/J F1 hybrid males and PWKxDBA/2J F1 hybrid males differ substantially in sperm count and relative combined testes weight despite sharing known sterility alleles. These findings suggest that unknown hybrid male sterility alleles segregate both between and within mouse subspecies.