The genetic architecture of resistance and susceptibility to virulent ovine footrot was studied in a cohort of 3,208 animals from 37 informative flocks of predominant Merino (93%), and Merino Types (Poll Merino, Dohne and South African Meat Merino). Footrot was scored as a binary trait where an animal was scored as affected (1) or unaffected (0, free from footrot), after 2 known challenges. For final analysis, animals from flocks with a prevalence in the range of 30-70% were selected. Animals were genotyped with either a 50K or 15K SNP panel on the Illumina Ovine bead array resulting in combined imputed SNP genotype for 51,713 markers for all animals. The animals were of mixed ages (lambs, yearlings, hoggets and adults), sexes, and breeds. Heritability of footrot was 0.39 ± 0.04 based on a genomic relationship matrix on the underlying scale. Corresponding proportional chromosome heritabilities were in the range of 0.00 ± 0.01 (OAR12) to 0.14 ± 0.04 (OAR23) and compared against expected based on chromosome length. Two markers on OAR23 accounted for a significant component of the additive genetic variance, whilst all residual SNP markers failed to reach statistical significance, despite being located on chromosomes with disproportionate effect on the genetic variance. The polygenic nature of genetic variation in resistance to footrot is discussed.