The koala (Phascolarctos cinereus) is an arboreal folivorous marsupial which forms the backbone of the Australian tourism industry. This iconic species is currently threatened by habitat destruction and removal, climatic induced changes, effects of urbanisation, and disease. While many studies have investigated the genetic basis of disease susceptibility in the koala, little is known about the role genetics may play in koala mate choice. Major Histocompatibility Complex (MHC) genes play an essential role in the adaptive immune response and have been found to influence mate choice in a wide range of organisms. Understanding whether this mate choice mechanism exists in the koala would assist captive breeding programs and help protect this vulnerable species. The aim of this study was to determine whether koalas exhibit MHC-dependent mate choice by genotyping a study population of koalas from San Diego Zoo at several MHC-linked microsatellite loci and correlating the genotypes with koala mate choice using detailed pairing records provided by the zoo. The results show that male koalas which are less heterozygous at MHC loci overall have a higher copulation success, however those that are heterozygous at MHCII DAB loci have a greater probability of producing offspring. Furthermore, females are more likely to breed with a male if they are more similar at MHCII DAB loci. These results demonstrate the complexity of the genetic basis of mate choice in koalas and may potentially aid future pairing recommendations in captive facilities.