Euglenozoa is a diverse group of protists that includes euglenids, kinetoplastids, diplonemids, and symbiontids, with phototrophic euglenids and parasitic trypanosomatids being the most extensively studied. Among these, Trypanosoma brucei is a key model organism for molecular and cellular parasitology, supported by well-established genetic tools. Among these, RNA interference (RNAi) is widely used for targeted gene knockdown and functional genomics. RNAi knockdown, combined with functional complementation using RNAi-resistant constructs provides a powerful means to confirm the specificity of RNAi-induced phenotypes and to assess the function of genes. This chapter outlines a detailed protocol for the functional complementation of RNAi growth phenotype using codon-exchanged, RNAi-resistant constructs. Using the essential glycosomal membrane protein PEX15 as an example, we demonstrate that both full-length and mutant variants can be tested for their function and the dissection of essential regions in a protein. This combined approach confirms gene essentiality, reveals the roles of specific protein domains, and provides a robust framework for studying protein function and interactions in trypanosomatids and other euglenozoans with a functional RNAi pathway.