Objective To investigate the prevalence and genetic evolutionary characteristics of Anaplasma capra in parasitic ticks in selected regions of Fujian Province. Methods Parasitic ticks were collected from domestic and wild animals (including murine, muntjacs, dogs, goats, hares, cattle, wild boars, and pigs) in Zherong County, Zhouning County, Fu’an City and Xiapu County of Ningde City and Pucheng County and Shaowu City of Nanping City from 2011 to 2024. Following morphological and molecular biological identification, genomic DNA was extracted from ticks and A. capra citratesynthase gene (gltA) gene was amplified using nested PCR assay. Positive PCR amplification products were sequenced and initially aligned by BLAST on National Center for Biotechnology Information (NCBI). Sequence alignment was performed using the software MEGA 11, and a phylogenetic tree was created using with the neighbor-joining method. Genetic diversity indices of A. capra gltA gene sequence were calculated using the software DnaSP 6.0, and a haplotype network was constructed using the software PopArt 1.7 after grouping sequences by region using the software Arlequin 3.5.2.2. Comparisons of proportions were done with chi-square test and Fisher’s exact test, and influencing factors were identified using a multivariate logistic regression model. Results A total of 650 ticks were tested, with the highest prevalence of A. capra infection on the muntjac body surface (19.11%, 30/157), followed by on cattle body surface 2/13, and there was a significant difference in the prevalence of A. capra infection in different hosts (χ² = 59.64, P < 0.01). The captured ticks were mainly adults, followed by nymphs. The highest prevalence of A. capra infection was detected in nymphs (15.38%, 8/52), followed by in adults (4.88%, 29/594), with no A. capra infection seen in larval ticks (0/2) or eggs (0/2), and there was no significant difference in the prevalence of A. capra infection in ticks at different developmental stages (χ² = 9.15, P < 0.05). The prevalence of A. capra infection was 7.99% (27/338) and 0.78% (2/256) in female and male adult ticks (χ² = 16.29, P < 0.01). The prevalence of A. capra infection was 5.86% (5/88) in ticks from Zherong County, 11.06% (23/208) in Zhouning County, 0/7 in Fu’an City and 0/7 in Xiapu County of Ningde City and 2.69% (9/335) in Pucheng County and 0/5 in Shaowu City of Nanping City, and there was no region-specific prevalence found (χ² = 15.74, P < 0.01). The prevalence of A. capra infection was 4.64% (7/151) in ticks sampled in summer, and 4.37% (9/206) in autumn, 7.34% (21/286) in winter, and no infection was detected in ticks sampled in spring (0/7) (χ² = 2.86, P > 0.05). Six hundred fifty ticks belonged to 14 species of 5 genera, and the overall prevalence of A. capra infection was 5.69% (37/650) in ticks. A. capra was detected in 7 tick species, with the highest prevalence in Ixodes ovatu (42.86%, 12/28), followed by in Haemaphysalis of unknown species in Fujian Province (31.58%, 12/38) (χ² = 83.16, P < 0.01). Multivariate analysis showed a significantly higher risk of A. capra infection in tick nymphs than in adult ticks (OR = 2.83, 95% CI: 1.15 to 6.94), and a lower risk of A. capra infection was seen in ticks from Nanping City than from Ningdu City (OR = 0.20, 95% CI: 0.08 to 0.50). BLAST analysis showed that the 37 sequences shared 97.88% to 98.92% identity with the A. capra reference sequence (GenBank accession number: OQ847085.1). Phylogenetic analysis revealed that the A. capra sequences from this study shared the closest relationship with sequences of A. capra from Qinghai Province. A total of 15 haplotypes were identified in sequences of A. capra from selected regions of Fujian Province, with overall haplotype diversity of 0.88 and nucleotide diversity of 0.009, and Hap1 to Hap3 were dominant haplotypes. Conclusion The prevalence of A. capra infection is high in parasitic ticks in selected regions of Fujian Province. Surveillance and management of tick-borne pathogens are recommended to be intensified.