Recently we described the occurrence of a new lethal Mendelian disorder brachygnathia, cardiomegaly and renal hypoplasia syndrome (BCRHS) in sheep. To identify the genomic region associated with the condition, affected and unaffected animals sourced from a single Polled Merino/Merino sheep flock were genotyped using the Illumina Ovine SNP50 BeadChip. Association mapping identified a region of approximately 1.1Mb on ovine chromosome 2 with significance (pr<5 e-06). All affected animals were found to share a single homozygous haplotype in the identified region. This study supports that BCRHS is controlled by a single autosomal recessive Mendelian locus and provides the basis for identifying the causative mutation/s and this will enable development a DNA test to identify carriers in the wider Merino sheep population. Understanding the molecular control of BCRHS may provide insight into the fundamental genetic control and regulation of the affected organ systems.