This paper reviews recent use of flow cytometry in studies on apomictic plant taxa. The most of apomictic angiosperms are polyploid, often differing in ploidy level from their sexual counterparts within the agamic complex. Flow cytometry is widely used for screening the ploidy levels of mature plants and their seed generated both in the field and in experiments. Routine ploidy screening often accompanied by molecular markers distinguishing individual genotypes are used to reveal novel insights into the biosystematics and population biology of apomictic taxa. Apomixis (asexual seed formation) is mostly facultative, operating together with other less frequent reproductive pathways within the same individual. The diversity in modes of reproduction in apomicts is commonly reflected in the ploidy structure of their progeny in mixed-cytotype populations. Thus, flow cytometry facilitates the detection and quantification of particular progeny classes generated by different reproductive pathways. The specific embryo/endosperm ploidy ratios, typical of the different reproductive pathways, result from modifications of double fertilization in sexual/apomictic angiosperms.Thus, the reproductive origin of seed can be identified, including autonomous or pseudogamous apomixis, haploid parthenogenesis and sexual reproduction, involving either reduced or unreduced gametes. Collectively, flow cytometry has been used to address the following research topics: (i) assessing the variation in ploidy levels and genome sizes in agamic complexes, (ii) detection and quantification of different reproductive modes in facultative apomicts, (iii) elucidation of processes in populations with coexisting sexual and apomictic biotypes, (iv) evolution of agamic complexes, and (v) genetic basis of apomixis. The last topic is of paramount importance to crop breeding: the search for candidate gene(s) responsible for apomixis is the main objective of many research programmes. A list of the angiosperm taxa that could provide model systems for such research is provided.