BBX proteins play important roles in all of the major light-regulated developmental processes. However, no systematic analysis ofBBXgene family regarding the regulation of photoperiodic microtuber formation has been previously performed in yam. In this study, a systematic analysis on theBBXgene family was conducted in three yam species, with the results, indicating that this gene plays a role in regulating photoperiodic microtuber formation. These analyses included identification theBBXgene family in three yam species, their evolutionary relationships, conserved domains, motifs, gene structure,cis-acting elements, and expressional patterns. Based on these analyses,DoBBX2/DoCOL5andDoBBX8/DoCOL8showing the most opposite pattern of expression during microtuber formation were selected as candidate genes for further investigation. Gene expression analysis showedDoBBX2/DoCOL5andDoBBX8/DoCOL8were highest expressed in leaves and exhibited photoperiod responsive expression patterns. Besides, the overexpression ofDoBBX2/DoCOL5andDoBBX8/DoCOL8in potato accelerated tuber formation under short-day (SD) conditions, whereas only the overexpression ofDoBBX8/DoCOL8enhanced the accelerating effect of dark conditions on tuber induction. Tuber number was increased inDoBBX8/DoCOL8overexpressing plants under dark, as well as inDoBBX2/DoCOL5overexpressing plants under SD. Overall, the data generated in this study may form the basis of future functional characterizations ofBBXgenes in yam, especially regarding their regulation of microtuber formationviathe photoperiodic response pathway.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09406-1.