Tumorous stem mustard is well known for its swollen stem from which pickled “Fuling Mustard” is made. The molecular mechanisms governing the formation of the modified swollen stems are still poorly understood. This paper aims to identify candidate genes involved in the developmental regulation of the swollen stems. We sought to map previously published transcriptome datasets for Brassica juncea, including those derived from swollen stems at four different developmental stages and a mutant variety without swollen stems. Using pairwise comparisons of the five datasets, we identified 31 368 differentially expressed genes (DEGs). A total of 55 DEGs related to plant hormone signal transduction and 259 continuously up- or downregulated transcription factors were identified during stem development using Gene Ontology (GO) analysis. Quantitative real-time PCR (qRT-PCR) results showed that the expressions of 12 important candidate DEGs were consistent with RNA-seq results. Our study provided digital gene expression profiling and a dynamic view of the swollen stem development process. Furthermore, we identified candidate genes for further studies on mechanisms of modified stem development in non-model species.