Application of molecular approaches has led to a significant progress on the knowledge of the epidemiology of Cryptosporidium spp. Nevertheless, molecular information on the occurrence of cryptosporidiosis in domestic small ruminants, especially in goats, are limited and restricted to the study of a modest number of isolates, mainly from diarrhoeic neonates. In order to determine the Cryptosporidium species present in healthy post-weaned and adult small ruminants from north-western Spain and to analyse a possible age-related distribution of species, faecal specimens were collected in sheep and goat farms without neonatal diarrhoea outbreaks the year before the sampling. Cryptosporidium spp. DNA was detected by SSU-rRNA PCR-RFLP, using restriction enzymes SspI, VspI and MboII. C. parvum and C. ubiquitum isolates were further characterized at the GP60 locus. Our results reveal that Cryptosporidium spp. is widely distributed in small ruminant farms (47.4-50.0%), although its prevalence is low in both hosts (5.9-6.0%). No significant differences in individual prevalence were detected between age groups. C. xiaoi and the zoonotic C. parvum and C. ubiquitum were identified. In sheep, C. parvum was the predominant species and its prevalence increased with age, in contrast to C. xiaoi; C. ubiquitum was an occasional finding in adults. In goats, C. xiaoi and C. ubiquitum were the most frequent species and slightly more prevalent in adults than in post-weaned kids, in contrast to C. parvum. Subtyping analysis of C. parvum isolates revealed the presence of IIaA15G2R1 and IIaA14G2R1 in sheep, whereas IIaA13G1R1 and IIdA17G1 were restricted to goats; only the C. ubiquitum XIIa subtype 3 was found. Although the prevalences detected are low, these values are probably underestimated due to, amongst others, the cross-sectional design of the study and the intermittent oocyst-excretion of post-weaned and adult small ruminants. Thus, these animals may play an important role in the appearance of cryptosporidiosis outbreaks in humans and domestic ruminant neonates and therefore should be considered as a potential threat to animal production and human health.