Fungicides which are not easily degradable have the greatest adverse effects on soil microbes. These pesticides negatively affect the growth and multiplication of fungi and bacteria and consequently cause the disturbance of the natural soil microbial balance. In this study two fungicide tolerant isolates of rhizobia; clover isolate (TA1) and peanut isolate (8) were assessed in their capacity to degrade Vitavax and Rizolex. The performance of these isolates in fungicides degradation was tested using the colorimetric assay for Rizolex and the HPLC analysis for Vitavax to detect the degradation products. Using HPLC analyses, the control sample showed specific peak indicating the Vitavax presence in the medium. The specific peak did not change in the control samples throughout the experiment.With the strainTA1 the specific peak of the Vitavax fungicides started to reduce as the incubation time goes on. The Vitavax fungicide did not degrade completely after 240 hours of incubation with rhizobial isolate. The Rizolex used in this study contained blend of Thiram (active ingredient of Rizolex) and Tolcofs methyl fungicides in 1:1 ratio. The biodegradation of Rizolex in the liquid media showed the formation of two new intermediates which were released into the medium indicating the degradation of the tested fungicide by peanut rhizobial isolate No. 8 in 48 hrs of incubation 45% of this compound was degraded. This work shows that the selection of fungicides tolerant rhizobial strains is important to protect the rhizobial inoculants from the toxic effect of the pesticides.