This study was carried out to observe inter-strain variation at molecular level in the two vaccinal types (B: 3, 4 and B: 6). The 85, 27 kDa major and 70 and 40 kDa minor proteins run on SDS-PAGE were common in both strains. The 50, 32 and 29 kDa major proteins were found in B: 3, 4 but absent in B: 6. SDS-PAGE profiles of outer membrane protein (OMP) showed that 26 minor bands were common. The 50 and 32 kDa major protein were found in B:3,4 and absent in B:6, while 46kDa minor protein was found in B:6 only. The spectral peaks of whole cells, envelope and OMPs could be differentiated between B: 6 and B: 3, 4 by FT-IR analysis. Spectral peaks of B: 3, 4 whole cells were at 644 cm-1 and at absorbance of 5.90, while B: 6 spectral peaks were observed at wave numbers 628, 640 and 651 cm-1 and absorbance at 0.35, 0.66 and 0.67 respectively. The spectral peak was found in B: 3, 4 OMPs at 646 wave number (cm-1), while spectral peaks for B: 6 OMPs were at 628, 640 and 651 wave number (cm-1)respectively.