The aim of this study was the evaluation of activities of versatile peroxidase (VP) in cultures of Clonostachys sp. (Gliocladium sp.) strains during biotransformation of 0.2% alkali lignin (AL). The principal component analysis (PCA) method was applied to determine the main factors and correlation between biotransformation of 0.2% AL, activity of VPs, pH value, and Clonostachys sp. strains. The biotransformation of 0.2% AL in cultures of microscopic fungi included decolorization (medium lightening) and colorization (darkening of the medium). The versatile peroxidase synthesized by the microscopic fungi tested showed activity for oxidation of Mn(II) and guaiacol, but the activity for oxidation of guaiacol in the presence of Mn(II) was significantly higher. The PCA analysis indicated a strong correlation between biotransformation of 0.2% AL and pH and between oxidation of Mn(II), guaiacol without and in the presence of Mn(II) ions, strains, and pH.