Samples of Cryptosporidium spp., collected in a cross-sectional study of calves (median age 26 days) from 41 farms in Cheshire, UK, underwent molecular typing. The aim was to determine naturally occurring species/genotypes and to investigate transmission pathways within a local area. Of 60 positive samples, 54 were sequenced at an 18S rRNA locus and 51 were typed at a GP60 locus. C. parvum was identified in 50 samples, three cases were C. bovis and one was Cryptosporidium deer-like genotype. Six GP60 subgenotypes were identified. One subgenotype (IIaA15G2R1) was highly prevalent throughout the study area. A single subgenotype was identified on 20/22 farms. Two subgenotypes were found on 2/22 farms. The spatial scan statistic detected a cluster of subgenotype IIaA15G2R1 comprising seven farms. This suggests local transmission of the parasite between farms. As most of the isolates detected were the potentially zoonotic C. parvum allele IIa, intervention strategies should be considered to reduce the threat to public health. Biosecurity measures may reduce transmission between farms and result in lower levels of environmental contamination.