Investigation of centromeres in the pathogenic yeast Candida parapsilosis, shows that the location of two centromeres are polymorphic within this species. The centromeres consist of large inverted repeats (IRs), surrounding unique sequences. New (neo) centromeres have emerged in one C. parapsilosis isolate even though the original CEN location is undamaged. The neocentromeres do not contain IRs, and have no obvious sequence features. Overall design: Regions in the genome where the variant histone H3 (Cse4) binds in Candida parapsilosis were identified by chromatin immunoprecipitation (ChIP). Three copies of a 9 amino acid epitope from Human influenza hemagglutinin (HA), were introduced near the N terminus of both Cse4 alleles using CRISPR-Cas9 editing together with a synthetic repair template. The epitope was introduced into Cse4 twice independently in two different strains – C. parapsilosis CLIB214, which is the type strain, and C. parapsilosis 90-137, originally isolated from orbital tissue. We analysed ChIP signals per chromosome in the immunoprecipitated Cse4-HA strains, control input chromatin and control un-tagged strains, generating 10 samples.