Centromeres function as a platform for the assembly of multiple kinetochore proteins and are essential for chromosome segregation. An active centromere is characterized by the presence of a centromere-specific histone H3 variant, CENP-A. Faithful centromeric localization of CENP-A is supported by heterochromatin in almost all eukaryotes; however, heterochromatin proteins have been lost in most Saccharomycotina. Here, identification of CENP-A (CENP-A L.s. ) and heterochromatin protein 1 (Lsw1) in a Saccharomycotina species, the oleaginous yeast  Lipomyces starkeyi,  is reported. To determine if these proteins are functional, the proteins in  S. pombe , a species widely used to study centromeres, were ectopically expressed. CENP-A L.s.  localizes to centromeres and can be replaced with  S. pombe  CENP-A, indicating that CENP-A L.s.  is a functional centromere-specific protein. Lsw1 binds at heterochromatin regions, and chromatin binding is dependent on methylation of histone H3 at lysine 9. In other species, self-interaction of heterochromatin protein 1 is thought to cause folding of chromatin, triggering transcription repression and heterochromatin formation. Consistent with this, it was found that Lsw1 can self-interact.  L. starkeyi  chromatin contains the methylation of histone H3 at lysine 9. These results indicated that  L. starkeyi  has a primitive heterochromatin structure and is an attractive model for analysis of centromere heterochromatin evolution.