Calmodulin-like (CML) proteins represent a diverse family of protein in plants, and play significant roles in biotic and abiotic stress responses. However, the involvement of citrus CMLs in plant responses to drought stress (abiotic stress) and arbuscular mycorrhizal fungi (AMF) colonization remain relatively unknown. We characterized the citrus CML genes by analyzing the EF-hand domains and a genome-wide search, and identified a total of 38 such genes, distributed across at least nine chromosomes. Six tandem duplication clusters were observed in the CsCMLs, and 12 CsCMLs exhibited syntenic relationships with Arabidopsis thaliana CMLs. Gene expression analysis showed that 29 CsCMLs were expressed in the roots, and exhibited differential expression patterns. The regulation of CsCMLs expression was not consistent with the cis-elements identified in their promoters. CsCML2, 3, and 5 were upregulated in response to drought stress, and AMF colonization repressed the expression of CsCML7, 9, 12, 13,20, 27, 28, and 35,and induced that of CsCML1, 2, 3, 5, 8, 10, 11, 14, 15, 16, 18, 25, 30, 33, and 37. Furthermore, AMF colonization and drought stress exerted a synergistic effect, evident from the enhanced repression of CsCML7, 9, 12, 13, 27, 28, and 35 and enhanced expression of CsCML2, 3, and 5 under AMF colonization and drought stress. The present study provides valuable insights into the CsCML gene family and its responses to AMF colonization and drought stress.