Despite many ecological and evolutionary studies, the history of several species complexes within the freshwater crustacean genus Daphnia (Branchiopoda, Anomopoda) is poorly understood. In particular, the Daphnia longispina group, comprising several large-lake species, is characterized by pronounced phenotypic plasticity, many hybridizing species and backcrossing. We studied clonal assemblages from lakes and ponds comprising daphnids from several species complexes. In order to reveal patterns of reticulate evolution and introgression among species, we analysed three data sets and compared nuclear, mtDNA and morphological divergence using animals from 158 newly established clonal cultures. By examining 15 nuclear and 11 mitochondrial (12S/16S rDNA) genetic characters (allozymes/restriction enzymes), and 48 morphological traits, we found high clonal diversity and discontinuities in genotypic and morphological space which allowed us to group clones by cytonuclear differentiation into seven units (outgroup D. pulex). In contrast to six groups emerging from nuclear divergence (related to three traditional species, D. cucullata, D. galeata, D. hyalina and three pairwise intermediate hybrids), a seventh group of clones was clearly resolved by morphological divergence: distinct mtDNA haplotypes within one nuclear defined cluster, ‘D. hyalina’, resembled traditional D. hyalina and D. rosea phenotypes, respectively. In other nuclear defined clusters, association between mtDNA haplotype and morphology was low, despite hybridization being bidirectional (reciprocal crosses). Morphological divergence was greatest between young sister species which are separated on the lake/pond level, suggesting a significant role for divergent selection during speciation along with habitat shifts. Phylogenetic analyses were restricted to four cytonuclear groups of clones related to species. mtDNA and nuclear phylogenies were consistent in low genetic divergence and monophyly of D. hyalina and D. rosea. Incongruent patterns of phylogenies and different levels of genetic differentiation between traditional species suggest reticulate evolutionary processes.