The ability to detect viable contaminants in cultures propagated from the original host-expression system ensures that the integrity and purity of seed banks, fermentation broths, and ultimately the final product are continually controlled and maintained. The method developed to detect such agents must be selective for a broad spectrum of microbes, which may be present at very low levels, while discriminating from the host organisms. Although Pichia pastoris strains are frequently used as cell lines for the expression of heterologous proteins, a method that is specific for monitoring culture purity has yet to be reported for this type of organism. An assay that is capable of recovering contaminating bacteria, fungi, and closely related yeast from cultures of P. pastoris at parts per million detection limits is described here.