In the present study we investigated the extra cellular synthesis of gold and silver nanoparticles by using the yeast Candida guilliermondii. The formation of noble metal nanoparticles was monitored by the UV-Visible spectroscopy. As prepared gold and silver nanoparticles showed distinct surface plasmon peaks at 530 nm and 425 nm respectively. Phase and morphology of the as synthesized materials were investigated by X-ray diffraction and electron microscopy techniques respectively. XRD patterns confirmed the formation of gold and silver nanoparticles with face centered cubic structures. Bio-TEM images showed the formation of near spherical, well dispersed gold and silver nanoparticles in the size range of 50-70 nm and 10-20 nm respectively. The biosynthesized nanoparticles were tested for their antimicrobial activity against five pathogenic bacterial strains. The highest efficiency for both gold and silver nanoparticles was observed against Staphylococcus aureus. A comparative study was also done to find the effect of chemically synthesized noble metal nanoparticles against the above test strains. Chemically synthesized particles had no antimicrobial activity against any of the pathogenic strains. The results obtained suggest that biosynthesized gold and silver nanoparticles can be used as effective antimicrobial agents against some of the potential harmful pathogenic microorganisms.