The peroxisome is an organelle whose quantity is tightly regulated in response to changes in metabolic status, and much knowledge has been accumulated regarding its dynamics. The turnover of peroxisomes through autophagic pathways, termed pexophagy, has been especially studied in several methylotrophic yeast strains capable of growth on methanol as a sole carbon source, which led to the identification of factors involved in pexophagy (Dunn et al., 2005; Sakai et al., 2006). In the methylotrophic yeast Pichia pastoris, several types of membrane dynamics during pexophagy can be visualized simultaneously under live cell imaging. The decrease of abundant peroxisomal proteins in the cell lysate can be used as a convenient indicator of the completion of pexophagy. In combination, these methods provide basic information for further analysis of pexophagy at the molecular level.