Giardia intestinalis and Cryptosporidium parvum are commonly acquired waterborne parasites but little is known about their transmission cycles with regard to humans and animals. Faecal samples were collected over two time periods within the Waikato region of New Zealand from dairy cattle and humans and all positive isolates were genotyped. Of the 724 faecal specimens examined (354 cows, 304 calves and 66 humans), 16 cows, 32 calves and 5 humans were positive for G. intestinalis. Phylogenetic group 1 was found in 26 G. intestinalis positive dairy cattle with 22 being group 2. One G. intestinalis positive human isolate was group 1 and four were group 2. Of the 724 faecal specimens examined two cows, 33 calves and 66 human specimens were positive for C. parvum. All 35 C. parvum positive dairy cattle exhibited the bovine genotype while the 66 positive humans showed a seasonal shift in the prevalent genotype with the bovine dominating the spring (100%) and the human dominating the late summer period (96%).