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Diversity assessment is a key factor to preserve and exploit the genetic resources of the environment. In order to contribute to the knowledge on genetic diversity of fungi for the biological control of insect pests of the Colombian coffee central zone, the populations of the Metarhizium spp. fungus were studied by means of molecular techniques. The assessment of genetic diversity was made by sequencing the transcribed spacer regions of the ribosomal genes (ITS) and the exons of region 3 of the beta-tubulin gene, and by amplifying polymorphic fragments in their restriction sites (AFLPs). Thirty-three isolates collected in the coffee zone were evaluated. Differences between organisms were analyzed by constructing similarity matrices from 203 AFLP markers, using the Jaccard index. The isolates were grouped by the UPGMA algorithm and the PCOORDA main coordinate analysis. The sequences of ITSs and beta-tubulin regions of isolates representative of the groups obtained were compared with existing sequences in the GenBank and analyzed by multiple alignment using CLUSTAL. The existence of three intra-specific groups for Metarhizium anisopliae, that have no relation with geographical origin, type of crop, or host was confirmed. The analysis of ribosomal DNA locates all the isolations obtained within the subspecies M. anisopliae anisopliae, with perfect condition in Clavicipetal Ascomycetes. Metarhizium had two beta-tubulin genes, which may correspond to two alleles or one family, but with taxonomic significance.