Accurate chromosome segregation is essential for eukaryotic cell division, ensuring the faithful transmission of genetic information and preventing aneuploidy. This process relies on the precise attachment of microtubules to kinetochores, multiprotein structures assembled on specific chromosomal regions known as centromeres. While functionally conserved, the composition of the kinetochore complex, especially the inner kinetochore, varies across eukaryotes. The inner kinetochore proteins interact with centromeric DNA, which is structurally diverse and rapidly evolving. Together, despite plasticity in organization and composition, the centromere-kinetochore complex works towards the shared goal of accurate chromosome segregation. Centromere diversity can be observed in budding yeasts, where centromeres vary from short, sequence-specific point centromeres to long, epigenetically maintained regional centromeres. However, our understanding of the inner kinetochore compositions remains limited in budding yeasts. Given their substantial centromere and genetic diversity, budding yeasts are an ideal group for studying the co-evolution of centromere structures and inner kinetochore compositions at the species level. To inventory inner kinetochore compositions in budding yeasts with varying centromere types, we developed “mign”, a tool written in Python, to automate the homolog identification of 20 inner kinetochore proteins across 338 species. The resulting inventory reveals that proteins binding to point centromeres in a sequence-specific manner are found in species with regional centromeres, even though regional centromeres lack sequence conservation and inherit centromere function independently of DNA sequence. Additionally, the inner kinetochore inventory in the Saccharomycodaceae family is similar to species with point centromeres, making them promising subjects for point centromere research. Discovering point centromeres in this family could imply an earlier origin of point centromeres than currently postulated. Exploring the co-evolutionary dynamics of centromeres and inner kinetochore compositions adds valuable insights into how distinct modes of genome evolution have shaped the diversity of kinetochores. Furthermore, understanding centromere and kinetochore plasticity is important for understanding their conserved role in chromosome segregation. Our data provide insights and guidance for future wet lab projects aimed at validating and characterizing inner kinetochore inventory in budding yeasts and conducting functional analyses of kinetochore proteins.