Beta-D-xylosidase (BXL) is the key rate-limiting enzyme for the complete degradation of xylan, which is the main component of hemicellulose in the plant cell wall. In this study, 16 genes encoding putative BXL proteins were identified in Brassica juncea genome. Protein physicochemical properties, gene structure and conserved motifs, chromosomal distribution and gene expression during stem swelling of BjuBXL family genes were analyzed. The results showed that 16 BjuBXL genes were classified into seven categories and formed two subfamilies according to the phylogenetic tree analysis. Subfamily 1 included BjuBXL1~5 and Subfamily 2 included BjuBXL6 and BjuBXL7. BjuBXL1-1~1-4 were closely related to AtBXL1, which was involved in the Arabidopsis cell wall metabolism and plant development. Multiple alignments of the 16 BjuBXL protein sequences revealed that all of them contained the conserved WGR and KH motifs that are associated with substrate binding and conserved amino acids at two key active sites for xylose hydrolysis. Sixteen BjuBXL genes coded 769 to 984 amino acids, which corresponding 83.37 to 109.32 kD molecular weight protein. The grand average of hydropathicity (GRAVY) score of the 16 BjuBXL proteins was predicted from -0.273 to -0.049, indicating these proteins are hydrophilic. According to gene structure and conserved motifs analysis, subfamily 1 of BjuBXL contained 5~11 exons and subfamily 2 contained 3~5 exons, and all the BjuBXL proteins contain ten conserved motifs. Chromosomal distribution analyses showed that 7 BjuBXL genes were located in 5 chromosomes of A subgenomes and 8 BjuBXL genes are located in 4 chromosomes of B subgenomes. The expression patterns of 16 BjuBXL genes during stem swelling was obtained from the RNA-seq data, 9 BjuBXL genes showed noticeable expression changes during the stem swelling process, while other 7 BjuBXL genes were nearly not expressed. The expression of BjuBXL1-1 and BjuBXL 1-2 were found notably correlated with stem swelling. Furthermore, real-time PCR results revealed that the transcriptional levels of BjuBXL1-1and BjuBXL1-2 were up-regulated during stem swelling and were significantly higher in the inner pith (P2~P4) than in regions of the outer pith of swollen stem (P1). Our results suggest that BjuBXL1-1 and BjuBXL1-2 may play an essential role in the inner pith cell wall metabolism during stem swelling. This study laid a foundation for further investigations of the function of BXL family genes in B. juncea var. tumida.