The guppy, Poecilia reticulata, a teleostean fish of the order Cyprino
dontiformes, has been used extensively in studies of host-parasite int
eractions, courtship behavior, and mating preference, as well as in ec
ological and evolutionary genetics. A related species was among the fi
rst poikilotherm vertebrates to be used in the study of histocompatibi
lity genes. All these studies could benefit from the identification an
d characterization of the guppy major histocompatibility complex (Mhc)
genes. Here, both class I and class II genes of the guppy are describ
ed. The number of expressed loci, as determined by representation of c
lones in a cDNA library, sequencing, and Southern blot analysis, may b
e low in both Mhc classes: combined evidence suggests that there may b
e one expressed class II locus only and one or two expressed class I l
oci. The variability of aquaristic guppy stocks is very low: only thre
e and two genes have been detected at the class I and class II loci, r
espectively, in the stocks examined. This genetic paucity is most like
ly the consequence of breeding practices employed by aquarists and com
mercial establishments. Limited sampling of wild guppy populations rev
ealed extensive Mhc polymorphism at loci of both classes in nature. Co
mparison of guppy Mhc sequences with those of other vertebrates has re
vealed the existence of a set of insertions/deletions which can be use
d as characters in cladistic analysis to infer phylogenetic relationsh
ips among vertebrate taxa and the Mhc genes themselves. These indels a
re particularly frequent in the regions coding for the loops of al and
alpha 2 domains of class I proteins.