Centromeres are rapidly evolving across eukaryotes, despite performing a conserved function to ensure high-fidelity chromosome segregation. CENP-A chromatin is a hallmark of a functional centromere in most organisms. Due to its critical role in kinetochore architecture, the loss of CENP-A is tolerated in only a few organisms, many of which possess holocentric chromosomes. Here, we characterize the consequence of the loss of CENP-A in the fungal kingdom. Mucor circinelloides, an opportunistic human pathogen, lacks CENP-A along with the evolutionarily conserved CENP-C but assembles a monocentric chromosome with a localized kinetochore complex throughout the cell cycle. Mis12 and Dsn1, two conserved kinetochore proteins, were found to co-localize to a short region, one in each of nine large scaffolds, composed of an ∼200-bp AT-rich sequence followed by a centromere-specific conserved motif that echoes the structure of budding yeast point centromeres. Resembling fungal regional centromeres, these core centromere regions are embedded in large genomic expanses devoid of genes yet marked by Grem-LINE1s, a novel retrotransposable element silenced by the Dicer-dependent RNAi pathway. Our results suggest that these hybrid features of point and regional centromeres arose from the absence of CENP-A, thus defining novel mosaic centromeres in this early-diverging fungus. •Mucorales have lost CENP-A and CENP-C, two essential components of the kinetochore•Mucor shows a monocentric arrangement of its kinetochore throughout the cell cycle•Its nine centromeres are a mosaic of point and regional centromeres•Grem-LINE1 retrotransposons surrounding the centromeres are being silenced by RNAi Mucor circinelloides lacks CENP-A and displays monocentric chromosomes with defined mosaic centromeres. Navarro-Mendoza et al. describe these mosaic centromeres as a hybrid of point and regional centromeres with a conserved, short DNA motif flanked by large stretches of Grem-LINE1 retrotransposons, a unique organization never described in fungi.