Multi-locus data have proven invaluable in phylogenetic reconstruction and species delimitation. However, the mixed genetic signal from different loci can make inference of evolutionary history challenging and may produce incongruences depending on analytical and marker choice. Aside from incomplete lineage sorting (ILS) following diversification events that have had little time for deep differentiation, the most common causes of incongruent phylogenies are genetic introgression confounding a bifurcating evolutionary trajectory. In this study, we used multi-locus analytical approaches on sequence data of nine loci from 80 individuals of over 20 Neotropical Elaenia flycatcher species to examine the systematics, molecular phylogeny and species limits of this complex genus. Our results provide a robust phylogeny and estimates of species limits within Elaenia, but point to important cases of incongruences among phylogenies based on different analytical approaches. Simulations and estimates of divergence times provide reasonable explanations for the incongruent placement of some Elaenia taxa, pointing to multiple cases of both ILS and introgression within the genus. Molecular dating of major evolutionary events revealed intensive diversification during the Pleistocene, suggesting a central role of climate oscillations in the evolution of Elaenia flycatchers.