Background: The gut microbiome affects the health and performance of the animal. This study was carried out to evaluate the effect of Alchornea cordifolia and Costus afer leaf meal on gut microbiome of young male rabbits. Methods: Twenty-four 5-6 months old rabbit bucks with an average weight of 5.3 kg were used for this study. The completely randomized design was used and the rabbit bucks were distributed into four feeding /treatment groups (T) designated as T1 (the control fed with regular rabbit feed only), T2 (fed with Alchornea cordifolia), T3 (fed with Costus afer) and T4 (fed with a mixture of Alchornea cordifolia and Costus afer). The rabbits were fed the experimental diet for eight weeks and samples for microbiological analysis were collected from the different sections of the rabbit gut (stomach, ileum, caecum, and colon) and droppings then analyzed for total heterotrophic bacteria (THB) and total coliform counts (TCC). Results: The population density of THB was the highest in T4 at the stomach (5.03±0.87 x 105 colony forming units (CFU)/g) and ileum (5.32±1.19 x 105 CFU/g), but in T3 at the caecum (4.83±0.95 105 CFU/g), colon (4.15±0.60 x 105 CFU/g) and droppings (3.35±0.65 x 105 CFU/g. The population of TCC was highest in T4 in the stomach (i.e., 2.72±0.40 x 105 CFU/g) and ileum 2.67±0.53 x 105 CFU/g), in T3 at the caecum (3.53±0.69 x 105 CFU/g) and droppings (2.02±0.37 x 105 CFU/g, but T1 in the colon (2.77±0.60 x 105 CFU/g). The feed intake was the highest in T4, followed by T3 and T1, but the least in T2 (P 0.05) in the average weight gain of the rabbits (1.75 kg). Conclusions: We found that while Alchornea seemed to be reducing the population, Costus afer was enhancing their population and the overall effect on weight gain was insignificant.