In the present study, seven reference Bacillus species and a total of eighteen new facultative alkaliphilic Bacillus strains, isolated from the water of Lake Van and its soil surroundings, were identified using phenotypic characteristics and the numerical analysis of whole-cell protein profiles. According to morphological, biochemical and physiological characteristics, it was found that the new isolated strains belonged to Bacillus genus. In addition, the research indicated that SDS-PAGE of polypeptides of whole-cell extracts can provide more valuable taxonomic information than conventional tests based on the phenotypic characteristics at the species and subspecies levels. Numerical analysis of whole-cell protein profiles of test strains revealed 4 basic clusters (I-IV) at dissimilarity values of 18.9 % or above. The results of numerical analysis confirmed that each cluster had characteristic and distinctive protein profiles. Indeed, this study showed that the application of numerical analysis, coupled with the utilization of a standardized identification system instead of simple quantitative comparison of protein patterns, greatly enhanced the utilization of whole-cell protein profiles for identification of the facultative alkaliphilic Bacillus species.