The effects of homoeology and sex on recombination frequency were studied in crosses between cultivated pearl millet, Pennisetum glaucum, and two wild subspecies, P. violaceum and P. mollissimum. For the two wild x cultivated crosses, reciprocal three-way crosses were made between the F1 hybrid and an inbred line (Tift 23DB1). The three-way cross populations were mapped to produce a female map of each wide cross (where the F1 was the female) and a male map (where the F1 was the male). Total genetic map lengths of the two inter-subspecies crosses were broadly similar and around 85 % of a comparable intervarietal map. In the P. glaucumxP. mollissimum crosses, the map was further shortened by a large (40 cM) inversion in linkage group 1. Comparison of the recovered recombinants from male and female meiocytes showed an overall trend for the genetic maps to be longer in the male (∼10%) in both inter-subspecific crosses; however, analysis of individual linkage intervals showed no significant differences. Gametophytic selection was prevalent, and sometimes extreme, for example 12∶1 in favour of 'wild' alleles in the P. glaucumxP. mollissimum male recombinant population. One of the loci which determines panicle type in cultivated pearl millet and wild relatives, H, was mapped 9 cM from Xpsm812 on linkage group 7 in the P. violaceum cross.