Short interspersed repetitive elements (SINEs) have been shown to be excellent markers of molecular phylogeny, since the integration of a SINE at a particular position in a genome can be considered an unambiguous derived homologous character. In the present study, we isolated a new family of SINEs from cichlids in Lake Tanganyika, whose speciation and diversification have been regarded as prime examples of explosive adaptive radiation. Members of this new SINE family, which we named the AFC family, are about 320 bp in length, and each has a tRNA-related region in its 5' region, as do most of the members of SINE families reported to date. A dot blot hybridization experiment showed that this family is distributed extensively in the genomes of cichlids in Africa, with estimated copy numbers of 2 x 10(3)-2 x 10(4) per haploid genome. Our investigations of the patterns of insertion of members of this family at six orthologous loci demonstrated clearly that four previously identified tribes, namely, the Lamprologini, Ectodini, Tropheini, and Perissodini, each form a monophyletic group. These results provide a basis for the elucidation of the phylogenetic framework of the cichlid fishes in Lake Tanganyika.