The Cameroonian freshwater crab genus Louisea Cumberlidge, 1994 currently includes four threatened species: L. edeaensis (Bott, 1969) from Lake Ossa Island, L. balssi (Bott, 1959) from Mt. Manengouba, L. yabassi Mvogo Ndongo, von Rintelen & Cumberlidge, 2019 from the Ebo Forest zone, and L. nkongsamba Mvogo Ndongo, von Rintelen & Cumberlidge, 2019 from the Nlonako Ecological Reserve. We report here on collections of specimens of L. yabassi (from two new localities) and L. nkongsamba (from six new localities). The phylogenetic relationships of the four species of Louisea are currently unresolved. Here, we describe morphological variation within populations of both L. nkongsamba and L. yabassi that are supported by differences in characters of the carapace, mandible, thoracic sternum, and male second gonopods. In addition, three genetic lineages were found within L. nkongsamba that are supported by uncorrected p-distance and the haplotype network. No correlation, however, was found between the morphotypes within the species and the genetic lineages grouping populations of both of these species. Phylogenetic analyses based on three mtDNA loci (COI, 12S rRNA, and 16S rRNA) revealed divergence times of 5.6 million years ago (Ma) for when L. edeaensis diverged from L. balssi, 4.1 MA for when L. yabassi diverged from L. nkongsamba and L. edeaensis, and 2.48 MA for when L. yabassi diverged from L. nkongsamba. Immediate threats to these rare and threatened species of freshwater crabs and to the rainforest ecosystem upon which they depend include deforestation, habitat fragmentation, agricultural encroachment, pollution and firewood gathering. Our results indicate that IUCN Red List reassessments of extinction risk for these four species would likely result in changes of category for L. balssi and L. edeaensis (both might be upgraded from EN to critically endangered (CR)), and first-time assessments for L. yabassi and L. nkongsamba would likely place them both in the endangered (EN) category. Recognition of species boundaries and of subpopulations of species will prove useful when making informed conservation decisions as part of the development of species action plans.