The purpose of the current study was to compare natural microflora counts of mature green tomatoes as influenced by visual cleanness, and investigate ability of chlorine sanitizer to reduce different groups of natural microflora on the surface of tomatoes using overhead spray brush roller system. We hypothesized that natural microflora might not be equally affected, with vegetative Gram negative bacteria being more sensitive and soil-related Gram positive sporoforming bacilli and molds more resistant. Microflora from untreated visibly clean and visibly dirty tomatoes, as well as from visibly clean tomatoes after 30 seconds deionized water or 100 ppm chlorine treatments, was recovered and spread plated on Tryptic Soy agar, MacConkey agar, and acidified Potato Dextrose agar. Microflora from untreated and chlorine-treated tomatoes was non-specifically enriched and plated on agar with chlorine paper disc diffusion assay applied to check for inhibition zone differences. Interestingly, there was no significant difference in plate counts between visibly clean and dirty tomatoes (p >0.05). Chlorine was more effective than water alone to reduce microbial counts on tomatoes for all microbiological media tested. Based on similar relative reductions of microorganisms in each group, it was concluded that chlorine may have no preferential kill for investigated groups of microorganisms. High counts remaining after treatment with chlorine solution suggested possibility of resistant microbial biofilm formation on the surface of tomatoes.