In the present study, we obtained several bacterial isolates from direct plating (without enrichment) of the diluted extract of apples and oranges obtained from commercial market of major cities in Tamil Nadu, India. Based on the cultural growth characteristics in different selective media, the isolates were grouped into four groups. The 16S rRNA gene was amplified using universal primers. The expected amplified fragments were obtained in four isolates belonging to two culture groups and were sequenced. This resulted in the identification of Staphylococcus warneri and Bacillus pumilis in apples and B.flexus and B.subtilis in oranges. The different species of Bacillus are reported already as endophytes in plants and plant-derived produce. However, the occurrence of S.warneri is unusual. The observation emphasizes the need to further our understanding of the changing ecology of bacteria, particularly human pathogenic Staphylococcus, which has adapted to inner tissues of fruits. Practical Application: Identification and detection of human pathogenic bacteria like Staphylococcus in fresh fruits is applicable in creating awareness among the public about the route cause of foodborne illness because of consumption of unhealthful raw and unpasteurized juices. In addition, this study helps us to reevaluate the present production and handling practices of fruits. It also emphasizes the need for developing strategies based on a coordinated approach by the growers, distributors, retailers, importers and public health officials to eliminate or contain such human pathogenic bacteria in fresh fruits. © 2013 Wiley Periodicals, Inc.