Early in the process of speciation, reproductive failures occur in hybrid animals between genetically diverged populations. The sterile hybrid animals are often males in mammals and they exhibit spermatogenic disruptions, resulting in decreased number and/or malformation of mature sperms. Despite the generality of this phenomenon, comparative study of phenotypes in hybrid males from various crosses has not been done, and therefore the comprehensive genetic basis of the disruption is still elusive. In this study, we characterized the spermatogenic phenotype especially during meiosis in four different cases of reproductive isolation: B6-ChrX MSM , PGN-ChrX MSM , (B6 3 Mus musculus musculus-NJL/Ms) F 1 , and (B6 3 Mus spretus) F 1 . The first two are consomic strains, both bearing the X chromosome of M. m. molossinus; in B6-ChrX MSM , the genetic background is the laboratory strain C57BL/6J (predominantly M. m. domesticus), while in PGN-ChrX MSM the background is the PGN2/Ms strain purely derived from wild M. m. domesticus. The last two cases are F 1 hybrids between mouse subspecies or species. Each of the hybrid males exhibited cell-cycle arrest and/or apoptosis at either one or two of three distinct meiotic stages: premeiotic stage, zygotene-to-pachytene stage of prophase I, and metaphase I. This study shows that the sterility in hybrid males is caused by spermatogenic disruptions at multiple stages, suggesting that the responsible genes function in different cellular processes. Furthermore, the stages with disruptions are not correlated with the genetic distance between the respective parental strains.