The Congo Basin is a biologically diverse and dynamic terrestrial region composed of a central rainforest block flanked by savanna-forest ecotone. Embedded within this region are the Congo, Ogooué, and Sanaga which constitute the most biodiverse river systems in Africa. Although the Congo Basin is dominated by lowland forest, it also harbors a variety of terrestrial and freshwater ecosystems. Forests and associated savannas have been shaped by both abiotic and anthropogenic influences and differ in terms of their hydrology, elevation, and soil type. Current species distributions are complex and are thought to have been shaped by both historical and ecological factors. Major drivers of speciation are thought to have resulted from either geographic isolation through past refugia, riverine barriers or divergence across environmental gradients. Both genetic and genomic tools can help to refine taxonomy, identify unique evolutionary lineages, and understand the historical and ecological factors that have led to the rich biodiversity that we see today. Genetic tools are increasingly being applied to conservation efforts, including tracking and curbing the illegal wildlife trade. Genomic techniques also offer powerful means to preserve biodiversity in the face of climate change and identify populations with the greatest potential to adapt. This approach can inform placement of new protected areas to enhance species resilience and reduce extinction risk. Despite the potential of genomic tools, their integration into conservation planning remains in its infancy and will require expertise and long-term investment. Future efforts should focus on developing a road map for incorporating genomic data into conservation strategies along with fostering stronger communication between researchers and practitioners. Lastly, many species in the Congo Basin await discovery and for most groups, there is a backlog of species awaiting description. Developing regional expertise is needed to address this taxonomic impediment.