In this study, matrix-assisted laser desorption ionisation time of flight mass spectrometry (MALDI-TOF MS) was used to identify bacteria from environmental matrices. The aim of this work was to determine the efficacy of this rapid technique and the bacterial community of agricultural samples. Environmental samples included the collection of irrigation waters and manures, and bacteria from the surface of vegetables were also investigated. From food safety point of view, the investigation of these microbial communities is inevitable considering their potential hazardous impact on the food production chain. Altogether 235 bacterial isolates were identified with the most frequent genera being Pseudomonas, Bacillus, Acinetobacter and Aeromonas. Our results indicated that MALDI-TOF MS can be used to identify causative agents of foodborne illnesses, food spoilage and common plant pathogens. However, limitations of the rapid identification technique were also encountered as we obtained correct identification at species level for 30.2% and at genus level for 69.8% of the isolates.