The hemipteran whitefly Bemisia tabaci (Gennadius) is one of the most destructive pests damaging more than 600 agricultural crop species worldwide. The B and Q biotypes are most widely spread in Korea but they are not distinguishable based on morphological characters. In order to search for protein markers that can be employed for rapid and accurate diagnosis of biotypes, two-dimensional PAGE (2DE) in conjunction with mass spectroscopic analysis were conducted. Eleven biotype-specific spots were repeatedly identified during three repetitions of 2DE and analyzed by Q-TOF. One of the B type-specific protein spots was identified as carboxylesterase 2 (Coe2). The transcript level of coe2 was determined to be 6 times higher in B type than in Q type by quantitative real-time PCR. In addition, comparison of genomic DNA sequence of coe2 between B and Q types identified a biotype-specific intron, from which specific primer sets were designed. One-step PCR using these biotype-specific primers successfully distinguished the two biotypes in a high accuracy. Availability of the biotype-specific protein and DNA markers will greatly improve the detection of B. tabaci biotype in the field.