This record contains orthology predictions based on the Maker gene annotation of the tuatara (Sphenodon punctatus) and a set of 25 other species, using the Ensembl methodology. See http://doi.org/10.5281/zenodo.1489354 for the Maker annotation in GFF format. The files all_trees.emf.gz and all_homologies.tsv.gz contain the phylogenetic trees (all_trees.emf.gz, in the EMF alignment format) and the derived pairwise orthologies and paralogies (all_homologies.tsv.gz, in tabular format). From the phylogenetic trees, sets of 1-to-1 orthologues across all 26 species were extracted (pure_one2one_orthologies.txt). Sets of orthologues that span all the species but include paralogues were reduced to 1 copy per species using gene order conservation and sequence similarity. This extra dataset is available in promoted_one2one_orthologies.txt The main Ensembl entry point for tuatara is: http://www.ensembl.org/Sphenodon_punctatus/ This work is supported by Ngatiwai iwi, Allan Wilson Centre, University of Otago, New Zealand Genomics Limited, Illumina, National eScience Infrastructure (NeSI NZ).