In this study, we investigated the expression of seven MYB transcription factors (a total of 17 genes that included Dof1.1, IQD1-1, MYB28, MYB29, MYB34, MYB51, and MYB122 and their isoforms) involved in aliphatic and indolic glucosinolate (GSL) biosynthesis and analyzed the aliphatic and indolic GSL content in different organs of Chinese cabbage (Brassica rapassp. Pekinensis). MYB28 and MYB29 expression in the stem was dramatically different when compared with the levels in the other organs. MYB34, MYB122, MYB51, Dof1.1, and IQD1-1 showed very low transcript levels among different organs. HPLC analysis showed that the glucosinolates (GSLs) consisted of five aliphatic GSLs (progoitrin, sinigrin, glucoalyssin, gluconapin, and glucobrassicanapin) and four indolic GSLs (4-hydroxyglucobrassicin, glucobrassicin, 4-methoxygluco-brassicin, and neoglucobrassicin). Aliphatic GSLs exhibited 63.3% of the total GSLs content, followed by aromatic GSL (19.0%), indolic GSLs (10%), and unknown GSLs (7.7%) in different organs of Chinese cabbage. The total GSL content of different parts (ranked in descending order) was as follows: seed > flower > young leaves > stem > root > old leaves. The relationship between GSLs accumulation and expression of GSLs biosynthesis MYB TFs genes in different organs may be helpful to understand the mechanism of MYB TFs regulating GSL biosynthesis in Chinese cabbage.