Faecal specimens from diarrhoeic pre-weaned calves (n=61) and lambs (n=127) collected over a 1-year period (2008-2009) at 27 cattle and 28 sheep farms in Galicia (NW Spain) were examined for the presence of Cryptosporidium oocysts and positive specimens were selected for molecular examination. Overall, 30 calves (49.2%) and 39 lambs (30.7%) tested positive for Cryptosporidium by microscopy. PCR products of the SSU rRNA locus were obtained for 27 Cryptosporidium positive calf isolates and 23 lamb isolates. Restriction analyses generated profiles of C. parvum in all isolates except for 9 lamb specimens from 5 farms that yielded banding patterns and sequences indicative of the Cryptosporidium cervine genotype. Sequence analyses of the glycoprotein (GP60) gene revealed that all but 1 C. parvum isolate from calves belonged to the subtype IIaA15G2R1 and 1 isolate was identified as the novel subtype IIaA13G1R1. Two different subtypes were identified in sheep flocks including IIaA16G3R1, which was seen in 7 lamb isolates from a single farm and subtype IIaA15G2R1, identified in 3 isolates from 2 farms. These findings suggest a limited genetic diversity within C. parvum in ruminant livestock from this geographical area, although both calves and lambs should be considered as a reservoir for zoonotic subtypes.