Abstract Background There are no studies of potential zoonotic diseases in Mapuche communities’ horses. Objectives The objective of this study was to determine the prevalence of Cryptosporidium in horses of the Mapuche communities. Study design This was a cross‐sectional study. Methods Faecal samples from 100 randomly selected horses (n = 100) were taken from rural Mapuche communities from four municipalities from the Araucanía Region. These samples were processed with the modified Ziehl‐Neelsen staining technique and grouped by sex, age and municipality. Results The general prevalence of Cryptosporidium spp. was 67.0% (n = 67). The prevalence was 51.0% (n = 51) in males and 49.0% (n = 49) in females, and there is no gender association to the presentation of Cryptosporidium spp. The prevalence by municipality was 60.0%, 80.0%, 64.0% and 64.0% in Curarrehue, Lonquimay, Padre las Casas and Teodoro Schmidt, respectively. The above shows no significant association between the sector and the presence of Cryptosporidium spp. The prevalence by age was 95.4% of horses tested positive for Cryptosporidium between birth and 6 years of age. About 27.3% of horses were tested positive in the age group between 7 and 10 years. There was no presence of Cryptosporidium spp. in the age group older than 11 years, showing a significant relationship between the age of the animal and the presence of Cryptosporidium ( P ˂ 0.05). Main limitations The sample analysis did not specifically identify the type of Cryptosporidium, and it was not possible to evaluate the zoonotic risk in the Mapuche communities. Conclusions Cryptosporidium spp. is present in working horses in Mapuche communities, with a 67.7% general prevalence, and there is a significant association between this parasite and the age of the horses, being higher in the age group between 0 and 6 years, with a prevalence of 95.4%. There may be a potential zoonotic risk in the Mapuche communities.