Cichlid fishes of the East African Rift Valley lakes constitute an imp
ortant model of adaptive radiation. Explosive speciation in the Great
Lakes, in some cases as recently as 12400 years ago, generated large s
pecies flocks that have been the focus of evolutionary studies for som
e time. The studies have, however, been hampered by the paucity of bio
chemical markers for phylogenetic reconstruction. Here, we describe a
set of markers which should help to alleviate this problem. They are t
he class I genes of the major histocompatibility complex. We provide e
vidence for the existence of at least 17 class I loci in cichlid fishe
s, and for extensive polymorphism of three of these loci. Since the po
lymorphism has a trans-species character, it will be possible to use i
t in investigating the founding events of the individual species. The
sequences of the cichlid class I fishes support the monophyly of actin
opterygian fish on the one hand, and of tetrapods on the other.