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The avocado belongs to the genus Persea, which is one of the most controversial genera of the Lauraceae family, since the relationships within the subgenus Persea are not clear and only recognized two species, Persea americana and Persea schiedeana. Its relationship with the subgenus Eriodaphne is also complex and there is a debate as to whether it is an independent genus. For this reason, the study aims to analyze the phylogenetic relationships within the genus Persea, with an emphasis on the subgenus Persea, using maximum parsimony and bayesian inference with the sequence of eight different fragments from nuclear, chloroplast and mitochondrial DNA. Sequences of the chloroplast ndhF, rbcL, matK, rpoC, trnH-psbA; mitochondria atp4 and cox3 and nuclear 18S rRNA were used. Fourteen fixed mutations were found in species of the subgenus Eriodaphne. The maximum parsimony and bayesian phylogenetic analyses of the super-matrices of the five chloroplast sequences and the eight concatenated ones, separated the members of both subgenera into two different clades with high bootstrap and posterior probability support, suggesting that the origin of Persea is not monophyletic and therefore both subgenera, Persea and Eriodaphne, could be recognized as phylogenetically independent genera.