As a supporting resource to our study of recombination in threespine stickleback fish (Gasterosteus aculeatus) (Roesti et al. 2013), we provide the full FASTA sequence of the reassembled reference genome (Dryad digital repository, doi:10.5061/dryad.846nj). In that reassembly, scaffolds originally anchored in the correct chromosome but in incorrect sense (visualized in grey in Appendix S1), and scaffolds previously unanchored but to be integrated in reverse sense (visualized in red in Appendix S1), were accidentally reversed only. Correctly, however, reverse-complementing these sequences is required. This mistake has no consequence to any analysis performed in our paper, because we simply recalculated marker positions based on the reassembly for our study. However, sequence-based analyses (i.e. alignment or BLAST searches) using our reassembled genome will be affected by the omission to reverse-complement. For this reason, we have reimplemented all the corrections visualized in Appendix S1, but this time reverse-complementing all scaffolds to be inverted. This new genome version, called ‘G.ac_2006_corrected_v2.fa’, is the one now provided on the Dryad site given above. We kindly thank A. Chaturvedi, A. Böhne and Z. Musilová for bringing this issue to our attention.