Bovine babesiosis is a tick-borne disease of major veterinary and economic importance, yet molecular epidemiological data from Kazakhstan remain limited. This study investigated the prevalence, distribution, and species composition of Babesia spp. in cattle across all 17 administrative regions of Kazakhstan. A total of 6455 cattle blood samples from 171 villages were screened by nested PCR targeting the cytochrome b (cytb) gene, and positive samples were characterized by sequencing and phylogenetic analysis. The overall positive rate for Babesia spp. were 3.87% (95% CI: 3.41–4.37%). Of 250 PCR-positive samples, 215 yielded high-quality sequences and were assigned to four species: Babesia major (31.2%), B. occultans (29.6%), B. bigemina (18.0%), and B. bovis (7.2%). Marked regional heterogeneity was observed, with B. major and B. occultans predominating across most regions, whereas B. bigemina was dominant in Atyrau. Turkistan was the only region where all four species co-circulated. First molecular evidence of B. bovis and B. bigemina was obtained for Atyrau, Akmola, and West Kazakhstan regions. These findings expand current knowledge of bovine babesiosis in Kazakhstan and reveal a species composition dominated by B. major and B. occultans, contrasting with the B. bovis/B. bigemina-dominated patterns commonly reported elsewhere. The detection of pathogenic Babesia species in previously unsurveyed regions highlights the need for continued molecular surveillance.

In Kazakhstan, despite the diversity of ixodid ticks and extensive livestock movement throughout Central Asia, ovine Babesia infections are poorly characterized. The objective of this study was to determine the occurrence, genetic diversity and geographic distribution of Babesia spp. in sheep from southern and southeastern Kazakhstan. A total of 1458 blood samples from 51 settlements across five regions were screened by nested PCR targeting mitochondrial cytb. Positive samples were characterized by Sanger sequencing, with additional multilocus analysis based on 18S rRNA and mitochondrial cox1 sequences. Babesia DNA was detected in 75/1458 samples (5.1%), with variation in PCR positivity among regions. Positive samples occurred in Turkestan (3.6%), Jambyl (7.2%), and Almaty (21.2%), but not in Kyzylorda or Jetisu. Phylogenetic analyses identified two geographically structured lineages. Nine Turkestan samples formed a lineage related to the Babesia sp. Xinjiang/Dunhuang group and were provisionally designated Babesia sp. TRK. The remaining 66 samples formed a B. motasi lineage comprising five cytb genotypes and showing closer affinity to the Lintan/Tianzhu group than to the Hebei/Ningxian group. Despite high 18S rRNA identity with B. motasi, mitochondrial markers revealed substantial divergence. The findings of the current study expand understanding of ovine Babesia diversity in Central Asia and emphasize the need for genomic characterization to resolve the taxonomic status of the detected lineages.