Amino acid/auxin permease (AAAP) is a transcription factor with a highly conserved amino acid region that regulates physiological processes and development in many plants and responds to various abiotic stresses. In this study, a genome-wide analysis of five legumes (Phaseolus vulgaris, Medicago truncatula, Lotus japonicus, Glycine max, and Cicer arietinum) identified 74, 106, 87, 147, and 70 AAAP genes, respectively. In addition, chromosomal localisation, phylogenesis, conserved motifs, gene structure, and gene replication analyses were performed on AAAP genes. The results showed that legume AAAP gene branches from the same evolutionary system had similar protein structures. In addition, by analysing the transcriptome data, we determined that the expression levels of AAAP differed in each tissue. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to investigate the expression patterns of AAAP under tissue-specific conditions. These results show that AAAP genes play crucial regulatory roles in tissue-specific gene expression. This study provides a basis for further exploration of the biological functions of the AAAP gene family in legumes. AAAP plays an important role in the growth and development of the five legumes. In particular, tissue-specific expression analysis provides a scientific basis for the development of agricultural production of these five legumes.