Abstract Cenchrus ciliaris L. is an apomictic forage grass grown in pastures and rangelands of the semi-arid tropics. It reproduces predominantly through apomixis; rarely, obligate sexual plants have also been reported. Absence of sexual reproduction limits the possibility of genetic improvement through hybridization. This study reports on hybridization of an obligate sexual, self-incompatible buffelgrass with pollen from apomictic plants towards development of an F2 population segregating for mode of reproduction and use of sequence characterized amplified region (SCAR) markers for screening the population. The segregation ratio of 3:1 (facultative: apomictic) was observed in the F1 generation, whereas it was 1:2:1 (apomictic: facultative: sexual) in the F2 generation. A number of obligate sexual F2 progenies with desirable agronomic traits were obtained. The SCAR markers were able to screen out apomictic plants from sexual ones, but failed to discriminate between facultative and sexual. Marker-assisted screening could be useful for introgression of desirable trait(s) in the apomictic genotype through hybridization.