The genomic processes enabling speciation and the coexistence of species in sympatry are still largely unknown. Here we describe the whole genome sequence of three closely-related species from the butterfly genus Morpho : Morpho achilles (Linnaeus, 1758), M. helenor (Cramer, 1776) and M. deidamia (Hübner, 1819). These large blue butterflies are emblematic species of the Amazonian rainforest and live in sympatry in a wide range of their geographical distribution. In addition they display parallel diversification of dorsal wing colour pattern, suggesting local mimicry. By sequencing, assembling and annotating their genomes, we aim at uncovering pre- and post-zygotic barriers preventing gene flow between these sympatric species. We found a genome size of 480 Mb for the three species and a chromosomal number ranging from 2n = 54 for M. deidamia to 2n = 56 for M. achilles and M. helenor. We also detected inversions on the sex chromosome Z that were differentially fixed between species, suggesting that chromosomal rearrangements may contribute to their reproductive isolation. The annotation of their genomes allowed us to recover at least 12,000 protein-coding genes in each species and to discover duplications of genes potentially involved in pre-zygotic isolation such as genes controlling colour pattern variation (bab) or colour discrimination (L-opsin). Altogether, the assembly and the annotation of these three new reference genomes open new research avenues into the genomic architecture of speciation and reinforcement in sympatry, establishing Morpho butterflies as a new eco-evolutionary model.