Pesticides are biologically active compounds designed to interfere with metabolic processes and environmental safety. The biodiversity of organophosphorus degrader bacteria in Mediterranean agricultural soils was evaluated. 47 strains were isolated from Sicilian soils under different management systems. The isolates were obtained from enrichment cultures containing parathion as an exclusive carbon source. They were grouped into 20 Operational Taxonomic Units (OTUs) on the base of the ribosomal Internal Transcribed Spacer (ITS) polymorphism. A positive and significative correlation was found between bacterial biodiversity and such soil chemico-physical characteristics (soil clay content, cationic exchange capacity, and carbon percentage). The strains, identified by partial sequencing of 16S rRNA gene, were tested in order to evaluate their pesticide degrading ability in Mineral Salt Medium (MSM) and in three different standard soils distinguished by their different chemico-physical characteristics. Solid Phase Micro-Extraction (SPME) and solid liquid extraction methods coupled with gas-chromatograph and mass-spectrometer (GC-MS) instruments were used. Strains affiliated to Sinorhizobium, Pseudoxanthomonas, Streptomyces iakyrus, Microbacterium takaoensis and Isoptericola dokdonensis have never mentioned as organophosphorus degraders.