The breeding of plantains (Musa species, AAB) in Nigeria has been approached through 4x – 2x breeding scheme to generate triploid hybrids. In this process, several factors were observed to impede rapid progress, including variations in genome size and structure within and across generations which reduces the accuracy of predicting progeny value from parental performance.  The objectives of the study were to, a) assess the potential of early screening of 4x (AAAB) - 2x (AA) Musa breeding populations for discriminating ploidy and genome classes based on Flow Cytometry and genome-specific RAPD analysis, b) study the relationship between parents and offspring from 4x-2x families using amplified fragment length polymorphism (AFLP), c) evaluate the agronomic performance of progenies of reciprocal (4x – 2x versus 2x – 4x) crosses in Musa to understand how gender or ploidy affect the inheritance of quantitative traits. The study was carried out at the High Rainfall Station of the International Institute of Tropical Agriculture in Onne (4º 43’ N, 7º 01’E, 10 m above sea level). Results indicated that progenies of 4x-2x crosses produced predominantly 3x progenies (94.1%). RAPD analysis identified seven genomic classes, dominated by AAA and AAB configurations segregating 1:1 (χ2 = 0.21, P = 0.05). Five AFLP +3 primer pairs produced 2158 polymorphic bands among the hybrids and parental lines with segregation distortion occurring in the population. The marker similarity index between hybrids in different families ranged from 33.0 to 90.0%, while the genetic distance (GD) ranged from 10% to 67%. The mean contributions of the 4x and 2x parents to their progenies were 0.9: 1.2, respectively. Diploid progenies predominantly produced from 2x – 4x crosses were shorter plants, took shorter time to flower and produced smaller bunches compared to 3x progenies from 4x - 2x crosses. The differences in reciprocal breeding outcomes were attributed to complex microsporogenesis in parents of higher ploidy level.