This study utilized a standardization and cluster analysis technique for the selection and classification of beneficial bacteria. A set of synthetic data consisting of 100 individual variables with three characteristics was created for analysis. The three characteristics assigned to each independent variable were designated to have different numeric scales, averages, and standard deviations. The variables were bacterial isolates at random, and the three characteristics were fermentation products, including cell yield, antioxidant activity of culture, and enzyme production. A standardization method utilizing a standard normal distribution equation to record fermentation yields of each isolate was employed to weight their different numeric scales and deviations. Following transformation, the data set was analyzed by cluster analysis. The Manhattan method for dissimilarity matrix construction along with complete linkage technique, an agglomerative method for hierarchical cluster analysis, was employed using statistical computing program R. A total of 100 isolates were classified into groups A, B, and C. In a comparison of the characteristics of each group, all characteristics in groups A and C were higher than those of group B. Isolates displaying higher cell yield were classified as group A, whereas those isolates showing high antioxidant activity and enzyme production were assigned to group C. The results of the cluster analysis can be useful for the classification of numerous isolates and the preparation of an isolation pool using numerical or statistical tools. The present study suggests that a simple technique can be applied to screen and select beneficial microbes using the freely downloadable statistical computing program R.