Cichlid fishes have been used as model organisms in research because they represent one of the most striking examples of rapid and convergent evolutionary radiation among vertebrates. Several genomic resources have been developed for African cichlids highlighting bacterial artificial chromosome (BAC) libraries, sex markers identified in linkage groups (LG) 1, 3, 5 and 7 and several genomes sequenced (Cichlid Genome Consortium), opening new avenues for comparative genomics. In this report, to address discussion on the evolution of sex linked markers identified in cichlids, we integrate genetic maps of LG 1, 3, 5 and 7 from Oreochromis niloticus to cytogenetic maps of several cichlids and conducted comparative analysis of cichlids with the fish model species, Tetraodon nigroviridis (pufferfish), Gasterosteus aculeatus (stickleback) and Oryzias latipes (medaka), and also with other vertebrates. The in silico comparative mapping showed the investigated LGs strongly conserved (mainly LG 5 and 7) among non-related fish groups and even conserved in mammals and birds chromosomes. Although fishes are known to have high rates of chromosomal rearrangements and probably low rates of synteny, it seems that large syntenic chromosome segments have been preserved from major changes in distant related vertebrates. With the advance of genomic research, cytogenetic maps will be valuable for integrating and organizing genetic, genomic, and cytological information. These results provide the base for further cytogenetic and genomic studies in fishes, especially in the Cichlidae family.