Galagete is a genus of microlepidoptera including 12 nominate species endemic to the Galapagos Islands. In order to better understand the diversification of this endemic insular radiation, to unravel relationships among species and populations, and to get insight into the early stages of speciation, we developed a phylogenetic reconstruction based on the combined mitochondrial cytochrome oxidase I (555bp) and II (453bp), and the nuclear elongation factor-1alpha (711bp) and wingless (351bp) genes. Monophyly of the genus is strongly supported in the Bayesian and maximum likelihood analyses suggesting a single colonization event by a common ancestor. Two cases of paraphyly observed between species are hypothesized to represent imperfect species limits for G. espanolaensis nested within the G. turritella clade, and introgressive hybridization or lineage sorting in the case of the population of G. protozona from Santa Fe nested within the G. gnathodoxa clade. A geologically calibrated, relaxed molecular clock model was used for the first time to unravel the chronological sequence of an insular radiation. The first split occurring within the Galagete lineage on the archipelago is estimated at 3.3+/-0.4million years ago. The genus radiated relatively quickly in about 1.8million years, and gives an estimated speciation rate of 0.8 species per million years. Although the colonization scenario shows a stochastic dispersal pattern, the arrival of the ancestor and the diversification of the radiation coincide with the chronological emergence of the major islands.