Female-limited polychromatism is frequent in many species of Odonata. Ischnura elegans has three colour morphs: one male-like coloured (androchrome) and two additional gynochrome brown morphs (infuscans and rufescens-obsoleta morphs). A total of 19 progenies obtained from once-mated females were reared in the laboratory in three generations. Results indicate that the colour morphs are controlled by the same genetic system as previously described for I. graellsii, i.e. an autosomal locus with female-limited expression and with three alleles with a hierarchy of dominance (pa > pi > p°). Five interspecific crossings between female I. graellsii and male I. elegans, five crossings between hybrid females and male I. elegans and one crossing between female I. graellsii and a hybrid male further confirmed that the genetic system is the same in both species. A survey of morph frequencies in north-west Spain revealed that I. elegans shows high variability in androchrome frequency (4–91%) between nearby populations, whereas in I. graellsii androchromes never are the majority morph (5–40%). The highest androchrome frequency in I. graellsii was found in populations closest to a locality where both species have hybridized, and that now has the highest androchrome frequency of I. elegans. We hypothesize that I. elegans genes have been incorporated into the genome of I. graellsii resulting in increased androchrome frequency in the latter species. Low androchrome frequency in I. elegans seems also related to the influence of I. graellsii genes. Therefore, we suggest that hybridization between both taxa is contributing to the temporal maintenance of contrasting androchrome frequencies in nearby populations. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 85, 471–481.