The Crenicichla mandelburgeri species complex from the Middle Parana basin is a diverse group of cichlid species and contains all known ecomorphs found within the entire genus Crenicichla. Here, we study the phylogenetic relationships within the C. mandelburgeri species complex using ddRAD sequencing with focus on its two candidate species flocks endemic to the Iguazu and Urugua-i Rivers, and on two putative sympatric species in the Piray Guazu River. These species flocks include four and three syntopic species, respectively, which are strongly adapted to different trophic niches and include derived ecomorphs of Crenicichla (molluscivores, a periphyton grazer, and a crevice-feeding thick-lipped invertivore). Our phylogenomic analyses strongly support monophyly and rapid diversification of the Iguazu species flock, but reveal more complex evolutionary histories in the Urugua-i and Piray Guazu tributaries. Most species in the Middle Parana, including one species in the Urugua-i and both species in the Piray Guazu show cytonuclear discordance, and in both of these tributaries, we also found hybridization in one of the resident species. Population-level analyses reveal complete isolation of the Iguazu species and coupled with their dramatic ecological diversity, this radiation exemplifies characteristics of a species flock that arose via ecological speciation.Facultad de Ciencias Naturales y MuseoComisión de Investigaciones Científicas de la provincia de Buenos Aires