Fungicides are one of the essential inputs in the improved technology for increasing crop production through crop protection. Copper fungicides Blitox and Fungimar are used widely as foliar sprays for control of many plant diseases. As major portion of fungicides applied to economically important crops eventually finds its way to soil, may disrupt the activities of microorganisms in the soil and thereby altering the biological equilibrium of soil. It is therefore planned to study the biological health of the soil with the help of viable counts of nine strains of Rhizobium japonicum after 21, 30 and 45 days intervals at 100 to 500 ppm concentrations of the two copper Fungicides. Results reveal that Blitox is more compatible than Fungimar to R. japonicum.