The relationship between neutral and adaptive genetic diversity is important to understand in assessing the implications of a population bottleneck. Fitness-related genes, such as those of the major histocompatibility complex (MHC), may be influenced by selection, and so retain diversity even when it is lost at neutral markers. We measured MHC class I variation in an archaic reptile species Sphenodon guntheri [North Brother Island (NBI) tuatara], which naturally occurs on one 4 ha island in Cook Strait, New Zealand, and has low levels of microsatellite diversity. MHC variation in S. guntheri was compared with microsatellite DNA variation, and with MHC variation in a large population of Sphenodon punctatus (Cook Strait tuatara) on Stephens Island. The NBI population shows significantly decreased levels of genetic diversity compared with the Stephens Island population. Only three different MHC sequences and three genotypes were found on NBI, compared with 15 sequences and 21 genotypes in a similar sample size from Stephens Island. Two sequences appear to be unique to the NBI population. The assortment of sequence variants into genotypes suggests strong gametic disequilibrium between two MHC class I loci in S. guntheri, and only two haplotypes that were present in Hardy–Weinberg proportions were identified. MHC diversity in NBI tuatara appears to be largely influenced by genetic drift, consistent with a recent population bottleneck. This may compromise the ability of this population to respond to novel disease threats.