Aluminum-activated malate transporters (ALMTs) have multiple potential roles in plant metabolism such as regulation of organic acids in fruits, movement of guard cells and inducing tolerance against aluminum stress. However, the systematic characterization of ALMT genes in loquat is yet to be performed. In the current study, 24 putative ALMT genes were identified in the genome of Eriobotrya japonica Lindl. To further investigate the role of those ALMT genes, comprehensive bioinformatics and expression analysis were performed. In bioinformatics analysis, the physiochemical properties, conserved domains, gene structure, conserved motif, phylogenetic and syntenic analysis of EjALMT genes were conducted. The result revealed that the ALMT superfamily domain was conserved in all EjALMT proteins. EjALMT proteins were predicted to be localized in the plasma membrane. Genomic structural and motif analysis showed that the exon and motif number of each EjALMT gene ranged dramatically, from 5 to 7, and 6 to 10, respectively. Syntenic analysis indicated that the segmental or whole-genome duplication played a vital role in extension of the EjALMT gene family. The Ka and Ks values of duplicated genes depicted that EjALMT genes have undergone a strong purifying selection. Furthermore, the expression analysis of EjALMT genes was performed in the root, mature leaf, stem, full-bloom flower and ripened fruit of loquat. Some genes were expressed differentially in examined loquat tissues, signifying their differential role in plant growth and development. This study provides the first genome-wide identification, characterization, and relative expression of the ALMT gene family in loquat and provides the foundation for further functional analysis.