In the eukaryotic cells, some cell organelles and membranes together make a membrane system called the endomembrane system. This system includes the endoplasmic reticulum, Golgi apparatus, lysosomes and nuclear membrane. Members of this system works together. They modify, package, and transport lipids and proteins. The lysosomes formed from Golgi apparatus and contains hydrolytic enzymes. Mitochondria is the site for cellualr respiration and is not a part of the endomembrane system.
Possession of flagellum is not a taxonomic feature. many different unrelated organisms have flagellum. euglena, zooflagellates but also some fungi or even human sperm cells.