The knowledge of the ichthyofauna remains an advantage and a privileged tool for a sustainable management of the fishery. The present study was carried out in three fisheries located in the upper basin of the Mouhoun River in Burkina Faso. The objective was to make a comparative study of the richness of the ichthyofauna present in the three fisheries during the rainy and dry seasons. Therefore, the sampling of fish was done on the basis of the daily catches of the fishermen. A total of 50 fishermen were selected, of which 30 in Samendeni, 10 in Balla and 10 in Bama.In all three fisheries 43 species distributed in 31 genera and 18 families were identified. The most representative families are:Cichlidae (66%), Osteoglossidae (9%), Claroteidae (5%), Mochokidae (4%) and Gymnarchidae (4%). The Samendeni fishery has the highest fish diversity followed by Balla and Bama with 34, 24 and 22 species respectively. The Kruskal Wally test shows that there is no significant difference (p-value=0.763) in terms of number of species between the dry and wet seasons. The p-values of the Chi-square test calculated give for the Shannon index 0.3608; Simpson's index 0.5577 and the Equitability index 0.5617 and show that there is no statistically significant difference in these indices between the two seasons. This study has shown that the upper Mouhoun basin contains a strong ichthyological diversity and that it is necessary to exploit it in a rational and sustainable way for the benefit of the communities.