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<i>Cryptosporidium parvum</i> is one of the major causes of neonatal calf diarrhoea resulting in reduced farm productivity and compromised animal welfare worldwide. Livestock act as a major reservoir of this parasite, which can be transmitted to humans directly and/or indirectly, posing a public health risk. Research reports on the prevalence of <i>Cryptosporidium</i> in ruminants from east Mediterranean countries, including Cyprus, are limited. This study is the first to explore the occurrence of <i>Cryptosporidium</i> spp. in cattle up to 24 months old on the island of Cyprus. A total of 242 faecal samples were collected from 10 dairy cattle farms in Cyprus, all of which were screened for <i>Cryptosporidium</i> spp. using nested-PCR amplification targeting the small subunit of the ribosomal RNA (<i>18S</i> rRNA) gene. The 60 kDa glycoprotein (<i>gp60</i>) gene was also sequenced for the samples identified as <i>Cryptosporidium parvum</i>-positive to determine the subtypes present. The occurrence of <i>Cryptosporidium</i> was 43.8% (106/242) with at least one positive isolate in each farm sampled. <i>Cryptosporidium bovis, Cryptosporidium ryanae</i> and <i>C. parvum</i> were the only species identified, while the prevalence per farm ranged from 20–64%. Amongst these, the latter was the predominant species, representing 51.8% of all positive samples, followed by <i>C. bovis</i> (21.7%) and <i>C. ryanae</i> (31.1%). Five <i>C. parvum</i> subtypes were identified, four of which are zoonotic—IIaA14G1R1, IIaA15G1R1, IIaA15G2R1 and IIaA18G2R1. IIaA14G1R1 was the most abundant, representing 48.2% of all <i>C. parvum</i> positive samples, and was also the most widespread. This is the first report of zoonotic subtypes of <i>C. parvum</i> circulating in Cyprus. These results highlight the need for further research into the parasite focusing on its diversity, prevalence, host range and transmission dynamics on the island.