This study aimed to investigate the effect of PSP (Pomegranate Seed Pulp) on rumen fermentation, digestibility, and methanogens and protozoa population (by competitive PCR) of the camel and goat rumen fluid. Treatments included 0, 5 and 10% PSP replaced wheat bran. Rumen fluid was collected from 3 goats and 2 camels according to the similarity of sex, breed, origin and time and used for three gas production tests. DNA extraction was performed by RBB + c method, band intensities (target and competing DNA) were calculated by the ImageJ program and line gradients were plotted based on the number of copies and intensity. Diets had no significant effect on methanogen and protozoa population (P < 0.05), but Based on numerical counting, diet containing 5% PSP reduced the microbial population. Animal species affected microbial populations so that both populations in camels were less than goats (P < 0.05). The production of gas and volatile fatty acids was not affected by diets. These two parameters and NH3 concentration and methane production in goats were higher than camel (P < 0.05). The pH digested dry matter and microbial protein in camels were higher than in goats (P < 0.05). Therefore, the competitive PCR technique is an effective method for the enumeration of Rumen microbiota. Dietary supplementation with pomegranate seed pulp can modify the methanogen and protozoa population, reduce methane production and increase microbial protein will improve the animal's energy resources and feed protein. This supplementation can be considered as a strategy to achieve performance and environmental benefits.