Sex determination in mammals is dependent on the presence of SRY, which codes for a protein with a DNA binding motif (the HMG-box domain). Here we analyze the evolution of SRY among seven genera of New World monkeys belonging to the family Cebidae. Estimates of the number of synonymous and nonsynonymous substitutions indicated the absence of positive selection acting on SRY evolution. The presence of indels at the C-terminus coding region in different genera and species maintained an open reading frame, indicating a selective pressure constraining the evolution of this coding region. Available data on the fertility of natural and captive interspecific hybrids failed to show any relationship between SRY evolution and speciation for the genera herein studied. Our phylogenetic arrangement for Cebidae genera was similar to previous topologies based on mitochondrial and autosomal DNA sequences. This arrangement also corroborated the division of Cebus into two species groups. However, for Callithrix the differences among SRY topology and those derived from autosomal and mitochondrial genes suggested a Y-chromosome ancestral polymorphism.