MYB family transcription factors have been proved to play an important role in biological process, such as plant growth and development, flavonoid synthesis, environmental stress, lignin biosynthesis. To explore if the MYB family members are involved in the lignin biosynthesis in Averrhoa carambola, a genome-wide bioinformatics analysis of R2R3-MYB transcription factor has been conducted, followed by the RT-qPCR analysis to valid the expression levels of the eight R2R3-MYB genes in twigs (T1, T3, T6), fruits and leaves at different stages. Fifty-seven 1R-MYB, 100 R2R3-MYB and four 3R-MYB have been identified. Out of them, 100 R2R3-MYB (AcMYBs) were detected to be unevenly distributed on 11 chromosomes and they were divided into 24 subclades (A1–A24; the genes from the same subclade present similarity on gene structures and functional motifs). The family gene expansion might associated to the segmental and tandem duplications, and the duplicated genes were undergone purifying selection. The sequence homology of R2R3-MYB gene family was observed in A. carambola, Arabidopsis thaliana and Populus trichocarpa. RT-qPCR showed that except for AcMYB05, the genes AcMYB41, AcMYB65, AcMYB84, AcMYB87, AcMYB92, AcMYB97 and AcMYB100 were found with higher expression in T3 and T6 and rare transcripts in T1, fruit and leaves. Collectively, the transcriptional profiles suggested the tissue-specific expression of seven AcMYBs, which possibly participate in the lignin biosynthesis pathway of A. carambola, therefore providing reference for further analyzing the MYB family members that interplay with the lignin biosynthesis.