This is the author accepted manuscript. The final version is available from Humana Press via the DOI in this record.The basidiomycete fungus Ustilago maydis has emerged as a powerful model organism to study fundamental biological processes. U. maydis shares many important features with human cells but provides the technical advantages of yeast. Recently, U. maydis has also been used to investigate fundamental processes in peroxisome biology. Here, we present an efficient yeast recombination-based cloning method to construct and express fluorescent fusion proteins (or conditional mutant protein alleles) which target peroxisomes in the fungus U. maydis. In vivo analysis is pivotal for understanding the underlying mechanisms of organelle m...