The waxy cuticle plays a very important role in plant resistance to various biotic and abiotic stresses and is an important characteristic of Welsh onions. Two different types of biangan Welsh onions (BG) were selected for this study: BG, a wild-type covered by wax, which forms a continuous lipid membrane on its epidermal cells, and GLBG, a glossy mutant of BG whose epidermal cells are not covered by wax. To elucidate the waxy cuticle-related gene expression changes, we used RNA-Seq to compare these two Welsh onion varieties with distinct differences in cuticular wax. The de novo assembly yielded 42,881 putative unigenes, 25.41% of which are longer than 1,000 bp. Among the high-quality unique sequences, 22,289 (52.0%) had at least one significant match to an existing gene model. A total of 798 genes, representing 1.86% of the total putative unigenes, were differentially expressed between these two Welsh onion varieties. The expression patterns of four important unigenes that are related to waxy cuticle biosynthesis were confirmed by RT-qPCR and COG class annotation, which demonstrated that these genes play an important role in defense mechanisms and lipid transport and metabolism. To our knowledge, this study is the first exploration of the Welsh onion waxy cuticle. These results may help to reveal the molecular mechanisms underlying the waxy cuticle and will be useful for waxy gene cloning, genetics and breeding as well as phylogenetic and evolutionary studies of the Welsh onion.