SPAG16 is the murine orthologue of Chlamydomonas reinhardtii PF20, a protein known to be essential to the structure and function of the “9 + 2” axoneme. The “9 + 2” axoneme provides the cytoskeletal core of all eukaryotic motile cilia and flagella. In Chlamydomonas, the Pf20 gene encodes a single protein present in the central pair of the axoneme. Loss of Pf20 prevents central pair assembly and results in flagellar paralysis. The murine Spag16 gene encodes two proteins. While 71 kDa SPAG16L is found in all murine cells with motile cilia or flagella, 35 kDa SPAG16S transcript and protein are detected only in male germ cells, suggesting a unique role distinct from general axoneme formation. Transgenic mouse studies published previously by our lab have shown that abrogation of both SPAG16 isoforms causes arrest of spermatogenesis, and the mutant allele is not transmitted to offspring by chimeric males. Mice homozygous for a knock-out of SPAG16L alone are infertile, but show no abnormalities in spermatogenesis. The defects seen in chimeric Spag16 mutant mice, unaccounted for by loss of SPAG16L, indicate a possible role for SPAG16S in the specialized process of male germ cell development. Our results demonstrate that SPAG16S is predominantly found in specific regions within the nucleus of round spermatids. These nuclear sub-domains also contain SC35, a known marker of nuclear speckles enriched in pre-mRNA splicing factors. Putative interaction partners of SPAG16S are also shown to play critical roles in the peri-nuclear region during the round spermatid transition to the condensation and elongation stage of spermiogenesis, the final specialization point in sperm development. The distinct localization of SPAG16S at this critical juncture, its interaction with discretely localized proteins at a critical temporal junction in spermatogenesis, and its ability to modulate SPAG16L expression, suggest that SPAG16S plays an important role in the gene expression machinery of male germ cells, and represents an evolutionary distinction in axoneme gene function.