French Guiana, part of the highly diverse Neotropical Region, hosts a significant level of freshwater fish endemism. It is composed of 8 rivers each demonstrating their own characteristics and environments, the Maroni being the boarder to the west and the Oyapock to the east. While previous studies have highlighted the high level of unique species in the Maroni Basin, our findings also revealed a higher than expected level of endemism, in the Oyapock Basin, suggesting a more distinct faunal composition than what was thought up to now. This study compares the freshwater fish communities in the Oyapock and Maroni Basins to better understand the community structures by analyzing morphological and genetic diversity, which were interpreted in terms of functional diversity. A total of 21 morphological traits were measured and analyzed in 1,515 fish specimens: 800 from the Oyapock Basin and 715 from the Maroni Basin. Principal Component Analysis (PCA) was used to study morphological variations and revealed strong similar structure between and within the two basins. In addition, COI gene sequencing was performed on 2,163 specimens (1,565 from the Maroni Basin and 598 from the Oyapock Basin) to assess their genetic diversity. Genetic distances and Principal Coordinate Analyses (PCoA) were computed, revealing structural similarities between the two basins. The results of these separate analysis led us to perform a combined analysis, in order to confirm the general trend of similar structure of the two basins despite their distinct faunistic assemblage. A RLQ analysis provided a comprehensive perspective on the connection between morphological traits and genetic distances among the fish species from both basins revealing a homogenous co-structure between both basins. The most significant variation was linked to the elongation and streamline body shape, while a secondary morphological gradient was emphasizing the robustness of body features and the size of the eyes. The analysis revealed 38 species common to both basins. Additionally, 42 sister species were identified between the Maroni and the Oyapock, along with a total 224 unrelated species. Our findings highlight the specialized adaptations of species in both the Oyapock and Maroni Basins, revealing that these adaptations are strikingly similar despite the distinct faunistic composition of each basin. This similarity underscores the crucial roles these species play in their respective ecosystems, demonstrating a parallel in how they have evolved to meet the ecological demands of their environments. Additionally, it underscored how the genetic divergence constraint, of the L table from our RLQ analysis, does not prevent the morphological structures, from the R and Q tables, to be strongly matched. Even though we are in presence of two distinct fauna between the Maroni and Oyapock Basins, the results show a highly similar co-structure between them. Our comprehensive analysis underscores the importance of combining different data sets to achieve a thorough understanding of biodiversity and highlights the need for conservation efforts to protect these distinct ecosystems.