Varroa destructor is a honey bee (Apis mellifera) parasite identified as one of the leading causes of overwintering colony loss in New Zealand. It has been shown that a naturally occurring heritable trait, "Varroa Sensitive Hygiene" (VSH), confers an advantage to colonies by increasing behaviours that limit the survival and reproduction of Varroa mites. The SNP 9-9224292 is an adenine/guanine (A/G) polymorphism on chromosome 9 of Apis mellifera where the G allele was observed to be associated with VSH behaviour in North American honey bees. In this study, we sought to determine if selection for the G allele of SNP 9-9224292 could decrease Varroa mite infestation of New Zealand honey bee (Apis mellifera ligustica) colonies. We genotyped queens and tracked their colonies over summer before measuring Varroa levels at the point of autumn Varroa treatment. The mean Varroa population level in colonies headed by queens that carry two copies of VSH associated G allele of SNP 9-9224292 was 28.5% (P<0.05) lower compared with colonies headed by queens with two copies of non-VSH associated A alleles. Although a significant reduction in mite infestation was achieved in treatment colonies, conventional Varroa treatment was still required for adequate Varroa control. Considering the open mating of queens used and a lack of drift control in this study, this VSH SNP shows promise for marker assisted selection of New Zealand honey bees when aiming for innate Varroa control traits.