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The result of phylogenetic analysis that uses molecular methods for the genus <i>Fusarium</i> is controversial by differences between obtained results when we analyzed amplicons from different genes; studying the DNA sequences, we obtain trees with splits that set different distribution for studied species. The present paper, explores the possibility of used micro-sequences of preserved genes for solving problems in the <i>Fusarium</i> phylogeny. Therefore, six <i>Fusarium</i> species isolated from the Bogota’s savanna (Colombia), responsible for the vascular wilt (<i>F. oxysporum</i>) and carnation basal rot (<i>F. avenaceum</i>, <i>F. culmorum</i>, <i>F. foetens</i>, <i>F. graminearum</i>, <i>F. verticillioides</i>) were evaluated using different genes: ITSs, α-Actin, β-Tubulin, COX, EF and Fumonisin. We found micro-sequences in the amplicons with highly preserved regions which are not useful for making phylogeny, this region have a CI (change index) between 0 and 0.29. Others regions (micro-sequences), that had a low number of changes in the nucleotide sequence with a CI between 0.3 to 0.79, when are analyzed using Neighbour Joining algorithm present a major difference between its, that other unpreserved regions with high percentages of changes (transitions or transversions) and CI between 0.8 and 1.0, that ended up having high phylogenetic similarity levels, showed between micro sequences of a single gene and between micro-sequences of different genes. These results are only a first approach for developing a model capable of identifying the micro-sequences on different genes that we can used to do bioinformatics and that produce the same phylogenetics relationship pattern in different analyzed regions. <p><p>Keywords: Fungus, Ornamentals, Perennial Ornamentals