This study presents a comprehensive proteomic analysis of the flagellar proteome of *Chlamydomonas reinhardtii*, a model organism for ciliary research. Using mass spectrometry, the researchers identified 360 proteins with high confidence and 292 with moderate confidence, resulting in a highly complete dataset. The flagellar proteome is rich in motor proteins, signal transduction components, and proteins with homologues linked to human diseases such as cystic kidney disease, male sterility, and hydrocephalus. The study also reveals that many proteins are conserved in humans but previously uncharacterized, highlighting the complexity of cilia and flagella. The dataset includes nearly all known flagellar proteins, with only a few exceptions due to gene absence or low expression. The analysis also shows that the flagellum contains glycolytic enzymes and proteins involved in ATP production, suggesting a role in energy metabolism. Additionally, the study identifies homologues of disease-related proteins in humans, emphasizing the importance of cilia in human health. The findings provide a valuable resource for understanding ciliary functions and their roles in disease.This study presents a comprehensive proteomic analysis of the flagellar proteome of *Chlamydomonas reinhardtii*, a model organism for ciliary research. Using mass spectrometry, the researchers identified 360 proteins with high confidence and 292 with moderate confidence, resulting in a highly complete dataset. The flagellar proteome is rich in motor proteins, signal transduction components, and proteins with homologues linked to human diseases such as cystic kidney disease, male sterility, and hydrocephalus. The study also reveals that many proteins are conserved in humans but previously uncharacterized, highlighting the complexity of cilia and flagella. The dataset includes nearly all known flagellar proteins, with only a few exceptions due to gene absence or low expression. The analysis also shows that the flagellum contains glycolytic enzymes and proteins involved in ATP production, suggesting a role in energy metabolism. Additionally, the study identifies homologues of disease-related proteins in humans, emphasizing the importance of cilia in human health. The findings provide a valuable resource for understanding ciliary functions and their roles in disease.