In addition to methanol, methylotrophic yeasts are capable of utilizing multicarbon substrates. Some key reactions of methanol, ethanol and fatty acid metabolism are located in specific organelles, microbodies (depending on enzymatic content they are termed more specifically as peroxisomes or glyoxysomes) whereas utilization of other multicarbon substrates, e.g. glucose, does not require participation of peroxisomes. Depending on metabolic demands, peroxisomes can grow, propagate or degrade. Numerous mutations leading to impairment of peroxisome biogenesis or altered regulation of this process are known. The mutations of methylotrophic yeasts Hansenula polymorpha and Pichia methanolica have been isolated which permit constitutive peroxisome biogenesis in the medium with glucose or ethanol and appear to be the regulatory mutations. Other mutations block biogenesis of peroxisomes even in the media with methanol and oleate. The methods for positive selection of the mutants of methylotrophic yeast Pichia pastoris defective in peroxisome biogenesis have been developed and the corresponding mutants have been characterized. The mutations leading to defect in peroxisome degradation of methylotrophic yeasts P. methanolica and P. pastoris have also been isolated. The corresponding mutations block peroxisome degradation after shift of methanol-grown cells to ethanol and/or glucose media due to the defects in vacuolar-dependent autophagy process.