In the present study, we identified and characterized the plant-specific WUSCHEL -related homeobox (WOX ) gene family that plays a major role in the determination of cell fate, early embryonic pattern formation, stem cell maintenance, organogenesis, flower development and somatic embryogenesis. For this purpose, the transcriptomes of four species of Phalaenopsis, namely P. aphrodite, P. modesta, P. bellina and P. lueddemanniana, were analysed, and nine PaWOX, ten PmWOX, eight PbWOX and nine PlWOX transcripts were identified. The duplication event analysis showed the presence of two duplication events in P. lueddemanniana, one each in P. bellina and P. modesta and no duplication event in P. aphrodite. During the evolutionary analysis, all the WOX proteins were clustered with those of Arabidopsis thaliana (AtWOX), Phalaenopsis equestris (PeWOX), Apostasia shenzhenica and Dendrobium catenatum (DcWOX). The expression analysis of the WOX genes suggested their critical role in floral development and in other developmental processes. The secondary and tertiary structural analysis of seven selected WOX proteins was then performed, with each protein representing its respective clade. The results provide a valuable resource for further studies of the molecular mechanisms of floral and vegetative developments in Phalaenopsis species.