Understanding the molecular mechanisms of sexual determination and differentiation in vertebrates is crucial to clarify the role of genes and their evolution in distinct taxa. For this purpose, the present work was focused on comparative evolutionary analysis of Foxl2 gene, a candidate that rules out the development of female sex in vertebrates, using a global domain view, including all genes of its multigenic family. This study included basal organisms, such as Chondrichthyes, and distinct groups besides vertebrates, such as Hemichordata, Urochordata, Cephalochordata, Mollusca, Insecta and Porifera. The phylogenetic recovering was based on the Bayesian and the maximum likelihood methods, performed in Beast and Phyml programs, respectively. First, a phylogenetic tree was generated including genes from the same domain family of Foxl2, called Forkhead, in all groups of eukaryotes available in Pfam database. This approach generated a phylogeny with 1,009 sequences, where Foxl2 was identified and used for posterior specific analysis. The generated trees exhibited two interesting results. First, for the global domain phylogeny, it was observed an unusual grouping of insects with chordates taxa. For now, we could speculate of a possible horizontal gene transference occurred for this group. Second, for the tree topology generated specifically for Foxl2 gene, it was showed that Chondrichthyes placed together with Tetrapoda, possibly due to the extra round of genome duplication occurred in Teleostei, which may have provided higher levels of sequence change in the course of evolution, when compared to the remaining vertebrates.