The basal haplochromine genus Pseudocrenilabrus comprises three valid species, although the current taxonomy most probably underestimates species richness. Previous phylogeographic studies on the P. philander species complex revealed a clear structuring of populations, shaped by river capture events. Here we report the discovery of P. cf. philander in Lake Chila, a small lake south of Lake Tanganyika. We were interested whether discrete morphs, similar to what has been found in Lake Mweru and the Lunzua River, were present in Lake Chila. We evaluated the phenotypic variability of the population in relation to other lacustrine and riverine populations by quantifying colouration and body shape. To place the specimens in a phylogeographic framework, we inferred a phylogeny based on the most variable part of the mitochondrial control region. We found two divergent mtDNA lineages in Lake Chila and tested for population structure and admixture between the lineages using microsatellite data. Our study reveals a complex phylogeographic pattern and demonstrates admixture of distant mtDNA lineages in Lake Chila, producing a hybrid swarm with substantial phenotypic variability. Unlike in Lake Mweru, Pseudocrenilabrus has not diversified further into discrete morphs in Lake Chila, probably because of the long-term instability of the lake and the presumed recency of the admixture event.