Moniliophthora roreri , is one of the most devastating cocoa disease in the Western Hemisphere. In Colombia, the disease is particularly severe in the Magdalena Valley, which is considered the possible center of origin for the pathogen species. We analyzed the genetic diversity of isolates from the departments of Santander, Antioquia, Tolima, and Huila in Colombia using 23 simple- sequence repeats (SSR) markers. In total, 117 different multilocus geno- types were found among 120 isolates, each one representing a unique haplotype. High mutation rates in the SSR and gene flow can explain the high levels of diversity. Also, the observed and standardized indexes of association ( I A and ¿ rd ) indicate that the populations of M. roreri are clonal. Furthermore, given the high haplotype diversity and the significant linkage disequilibrium observed, we hypothesize that M. roreri could be a primarily asexual species undergoi ng sporadic recombination or par- tial recombination through parasexuality. A Bayesian clustering analy- sis implemented by STRUCTURE showed that the most probable number of genetic groups in the data was three, confirming the geo- graphical differentiation among isolates. Similar results were obtained by a discriminant analysis of princip al components, a principal coordi- nate analysis, and a neighbor-joining tree from microsatellite loci base on Nei distance. Cacao genotypes and environmental variables did con- tribute to the genetic differentiation of the groups. We discuss how this information could be used to improve the management of FPR at the regional level.