AbstractDespite their essential role in the process of chromosome segregation in eukaryotes, kinetochore proteins are highly diverse across species, being lost, duplicated, created, or diversified during evolution. Based on comparative genomics, the duplication of the inner kinetochore proteins CenH3 and Cenp-C, which are interdependent in their roles of stablishing centromere identity and function, can be said to be rare in animals. Surprisingly, theDrosophila CenH3homologCidunderwent four independent duplication events during evolution. Particularly interesting are the highly diverged and subfunctionalizedCid1andCid5paralogs of theDrosophilasubgenus, which show that over one thousandDrosophilaspecies may encode twoCidgenes, making those with a single copy a minority. Given that CenH3 and Cenp-C likely co-evolve as a functional unit, we investigated the molecular evolution ofCenp-Cin species ofDrosophila. We report yet anotherCidduplication within theDrosophilasubgenus and show that not onlyCid, but alsoCenp-Cis duplicated in the entire subgenus. TheCenp-Cparalogs, which we namedCenp-C1andCenp-C2, are highly divergent. The retention of key motifs involved in centromere localization and function by both Cenp-C1 and Cenp-C2 makes neofunctionalization unlikely. In contrast, the alternate conservation of some functional motifs between the proteins is indicative of subfunctionalization. Interestingly, bothCid5andCenp-C2are male germline-biased and evolved adaptively. Our findings point towards a specific inner kinetochore composition in a specific context (i.e., spermatogenesis), which could prove valuable for the understanding of how the extensive kinetochore diversity is related to essential cellular functions.