Complexes of closely related cryptic species, that are indistinguishable mo
rphologically et have different ecology and host preferences, are widesprea
d in mosquitoes. The advantages of DNA-based methods of identification mean
that they have now largely replaced other methods of species determination
for such complexes. Here we discuss the relative merits of three different
approaches to species identification, all of which use amplification of th
e ribosomal RNA genes by die polymerase chain reaction. They include: restr
iction fragment length polymorphism in the Anopheles maculipennis complex f
rom the UK, allele-specific amplification in the An, dirus complex from Tha
iland; and single strand conformational polymorphism in the An. minimus com
plex from Thailand. The application of these methods is considered in the c
ontext of recent data on intraspecific genetic variation; geographic popula
tion structure and genetic introgression. (C) 1999 The Linnean Society of L
ondon.