The tribe Sciurini comprehends the genera <span name="style_italic">Sciurus</span>, <span name="style_italic">Syntheosiurus</span>, <span name="style_italic">Microsciurus</span>, <span name="style_italic">Tamiasciurus</span> and <span name="style_italic">Rheinthrosciurus</span>. The phylogenetic relationships within <span name="style_italic">Sciurus</span> have been only partially done, and the relationship between Mesoamerican species remains unsolved. The phylogenetic relationships of the Mesoamerican tree squirrels were examined using molecular data. Sequence data publicly available (12S, 16S, CYTB mitochondrial genes and IRBP nuclear gene) and cytochrome B gene sequences of four previously not sampled Mesoamerican <span name="style_italic">Sciurus</span> species were analyzed under a Bayesian multispecies coalescence model. Phylogenetic analysis of the multilocus data set showed the neotropical tree squirrels as a monophyletic clade. The genus <span name="style_italic">Sciurus</span> was paraphyletic due to the inclusion of <span name="style_italic">Microsciurus</span> species (<span name="style_italic">M. alfari and M. flaviventer</span>). The South American species <span name="style_italic">S. aestuans</span> and <span name="style_italic">S. stramineus</span> showed a sister taxa relationship. Single locus analysis based on the most compact and complete data set (i.e. CYTB gene sequences), supported the monophyly of the South American species and recovered a Mesoamerican clade including <span name="style_italic">S. aureogaster, S. granatensis</span> and <span name="style_italic">S. variegatoides</span>. These results corroborated previous findings based on cladistic analysis of cranial and post-cranial characters. Our data support a close relationship between Mesoamerican <span name="style_italic">Sciurus</span> species and a sister relationship with South American species, and corroborates previous findings in relation to the polyphyly of <span name="style_italic">Microsciurus</span> and <span name="style_italic">Syntheosciurus’</span> paraphyly. Rev. Biol. Trop. 62 (2): 649-657. Epub 2014 June 01. paraphyly. Rev. Biol. Trop. 62 (2): 649-657. Epub 2014 June 01.

phylogenetics; cytochrome B; Sciurus; Microsciurus; Syntheosciurus; Mesoamerica