This work aimed to study the dynamics of chromosome elimination from both parents in four interspecific hybrids (P1, H89, H40, and H42) originated from crosses between Napier grass (Pennisetum purpureum Schumach.) (2n = 4x = 28) and pearl millet [Pennisetum glaucum (L.) R. Br.] (2n = 2x = 14) after chromosome doubling. Large variation in somatic chromosome number was verified among and within hybrids. In P1 and H89, chromosome elimination was much less intense than in H40 and H42. Genomic in situ hybridization analysis revealed biparental and random elimination. The differences in chromosome number between P1–H89 and H42–H40 groups can be mainly attributed to the elimination of chromosomes from Napier grass. Higher ploidy level and homeology between genomes A and A’ are considered forces underlying the process of elimination. Effect of parental genotype is also taken into account to explain the differences in chromosome elimination. Potential of the partial hexaploid hybrids for Napier grass breeding is also discussed here.