Cowpea mosaic virus (CPMV) was analyzed by CZE and the two separated subcomponents recorded at similar to 2.2 and similar to 2.7 min were respectively designated to be the slow electrophoretic form of CPMV (CPMVs) and the fast electrophoretic form of CPMV (CPMVf) the two electrophoretic forms of CPMV, by the following methods: first, CZE analysis of the biospecific complexes of CPMV and anti-CPMV polyclonal antibody proved the properties of CPMV; second, isolation and CZE analysis of CPMVf and CPMVs. Because CPMVs was precipitated and CPMVf was left in the supernatant at pH 5.6, the only one peak at similar to 2.7 min from the supernatant was assigned for CPMVf, while the peak at similar to 2.2 min dominating for the precipite was deemed to be CPMVs. Third, viral characterization by directly analyzing the capsid proteins using MALDI-TOF-MS. Based on the theoretical molecular weights calculated from the sequence of the capsid proteins, the three peaks at m/z 21 516.75, 23 745.8 and 42 509.22 for natural CPMV were destined for the small (S) protein of CPMVf, the S protein of CPMVs and the large (L) protein of both of them, respectively. As expected, the non-appearance of the peak at m/z 23 745.8 for the isolated CPMVf sample indicated the absence of CPMVs, and the peak at m/z 23 745.8 was predominant in the spectrum for the precipitated CPMV, sample. After the confirmation of CPMVs and CPMVf, the CZE separation of them was optimized. The developed analysis method has proven useful in investigating the stability of CPMV and the effect of 2,4-dinitrophenyl-decoration on the modification of the electrophoretical behavior of CPMV.