The East African highland bananas (Musa spp. AAA), an important staple food in Uganda, are highly susceptible to the banana weevil (Cosmopolites sordidus Germar). Sources of host plant resistance to the banana weevil exist in wild diploid bananas. The use of wild diploid bananas to improve East African highland bananas can be facilitated by studying genetics of host plant resistance of inter-diploid crosses. The objectives of this study were a) to identify segregating weevil resistance and agronomic traits in an F2 diploid population, and, b) to determine the inheritance of banana weevil resistance and agronomic traits based on an F2 banana diploid population. An F1 population developed from Musa acuminata subsp. banksii acc. Kasaska (ITC0591) and M. acuminata subsp. microcarpa acc. Borneo (ITC0253) was selfed to generate an F2 diploid population. The F2 population was screened against weevil resistance and agronomic traits in the laboratory, pot and field experiments. There were significant differences (P < 0.05) among the different genotypes for banana weevil resistance traits such as head capsule width, body length, body weight, larval mortality, total damage, peripheral damage, dead weevils and larvae retrieved. There were also significant differences (P < 0.05) for agronomic traits such as inner corm hardness and total corm hardness. The histograms for the banana weevil resistance traits such as head capsule width, body length, body weight and larval mortality, total damage, peripheral damage, cross sectional inner and outer damage, larvae retrieved and dead weevils showed continuous distribution. Similarly, histograms for agronomic parameters such as height of plant at flowering and girth at 1 meter at flowering showed continuous distribution. The Chi-square test of goodness of fit indicated that weevil growth and damage parameters had significant modifications of the expected 9:3:3:1 ratio for two independent loci, thus suggesting epistasis affects their inheritance.