Little is known about the genetic of Cryptosporidium in calves in eastern regions of France. The aim of this study was to detect and isolate Cryptosporidium spp. in faecal samples from naturally infected pre-weanedcalves (≤ 45 days-old) in France. A total of 35 diarrhoeic pre-weaned calves faecal samples were collected from 26 dairy cattle farms with or without diarrhoea in 6 provinces. The screening was established microscopically by the detection of Cryptosporidium oocysts using an immunofluorescence (IF) staining method. IF-positive samples were then analysed to determine species by PCR-RFLP and sequencing targeting the 18S rRNA gene. C. parvum positive samples were subtyped through the analysis of the partial 60 kDa glycoprotein (gp60) gene. Data were then integrated into a phylogenetic tree analysis. IF revealed the presence of Cryptosporidium oocysts in 31 out of 35 (88%) samples. Combining results of 18S rRNA gene analysis, C. parvum was detected in 30 samples. Subtyping analysis in 27/30 samples (90%) of the C. parvum isolates revealed two zoonotic subtype families, IIa (24/27) and IId (3/27). Four subtypes were recognized within the subtype family IIa including IIaA15G2R1 (21/27) which is the hypertransmissible subtype the most frequently reported worldwide, IIaA17G3R1 (1/27), IIaA17G1R1 (1/27) and IIaA19G1R1 (1/27). Two subtypes were recognized within the IId subtype family including IIdA22G1 (2/27) and IIdA27G1 (1/27). These findings illustrate the high prevalence of Cryptosporidium in calves in dairy herds and increase the diversity of the molecular characteristics of C. parvum isolates with the first description of IIaA17G3R1, IIaA19G1R1 and IId subtypes in France. The presence of zoonotic subtypes of C. parvum species suggests that pre-weaned calves are likely to be an important reservoir for zoonotic C. parvum.