Duckweed species have a great potential to develop into fast-growing crops for water remediation and bioenergy production. Seed production and utilization of hybrid vigour are essential steps in this process. However, even in the extensively-studied duckweed species, Lemna gibba, flower primordia were often aborted prior to maturation. Salicylic acid (SA) and agar solidification of the medium promoted flower maturation and resulted in high flowering rates in L. gibba 7741 and 5504. Artificial cross-pollination between individuals of L. gibba 7741 yielded seeds at high frequencies unlike that in L. gibba 5504. In contrast to clone 7741, the anthers of 5504 did not dehisce upon maturation, its artificially released pollen grains had pineapple-like exine with tilted spines. These pollens were not stained by 2,5-diphenylmonotetrazoliumbromide (MTT) and failed to germinate. Therefore, clone 5504 is male sterile and has potential application with respect to hybrid vigour. Moreover, pollination of flowers of 5504 with 7741 pollen grains resulted in intraspecific hybrid seeds, which was confirmed by inter-simple sequence repeat (ISSR) markers. These hybrid seeds germinated at a high frequency, forming new clones.