Fundamental to understanding how biodiversity arises and adapts is whether evolution is predictable in the face of stochastic genetic and demographic factors. Here we show rapid parallel evolution across two closely related but geographically isolated radiations of Nicaraguan crater lake cichlid fishes. We find significant morphological, ecological and genetic differentiation between ecomorphs in sympatry, reflected primarily in elongated versus high-bodied shape, differential ecological niche use and genetic differentiation. These eco-morphological divergences are significantly parallel across radiations. Based on 442,644 genome-wide single nucleotide polymorphisms, we identify strong support for the monophyly of, and subsequent sympatric divergence within, each radiation. However, the order of speciation differs across radiations; in one lake the limnetic ecomorph diverged first while in the other a benthic ecomorph. Overall our results demonstrate that complex parallel phenotypes can evolve very rapidly and repeatedly in similar environments, probably due to natural selection, yet this evolution can proceed along different evolutionary genetic routes.