In this study we estimated the timing of speciation events in a group of angelfishes using hundreds of RADseq markers. The genus Holacanthus comprises seven species, including two clades of Panama trans-Isthmian geminates, which diverged approximately 3 Mya. These clades diversified within the tropical Eastern Pacific (TEP, three species) and tropical Western Atlantic (TWA, two species). Our data suggest that diversification occurred within the past 1.5 My in both ocean basins, but proceeded via different mechanisms. In the TEP, speciation was peripatric, while in the TWA, speciation is more likely to have occurred in sympatry. This study therefore highlights the use of RADseq markers for estimating both divergence times and modes of speciation at a 1-3 My timescale.