This paper continues a series of studies of the allogamous raphid diatom Achnanthes longipes, which has a complex reproductive system combining unisexual, bisexual and monoecious behaviour. Following earlier work on the effects of inbreeding in the progeny of crosses between two unisexual clones, we studied the progeny of clones that are capable of a high degree of selfing in monoclonal culture (‘monoecious clones’). Three generations of selfed progeny were examined. In addition, we investigated the F1 generation obtained after crossing two different monoecious clones. Monoecious clones produced monoecious or, more rarely, bisexual progeny, but did not give rise to unisexual progeny. As in inbred lineages made by crossing closely related unisexual clones, inbreeding in monoecious lineages leads to a reduction in the number of gametes formed by the gametangia, from two to one. Inbred clones exhibit marked inbreeding depression and only three inbred generations were possible in monoecious lineages. In the third, final inbred generation, monoecious sexual reproduction was initiated in monoclonal cultures but gametes rarely fused and none of the auxospores and initial cells that were formed were viable; this also occurred when the inbred clones were crossed with any of the other clones available. The significance of inbreeding and other aspects of the breeding system in A. longipes is discussed.