Euglenoid flagellates occur in most freshwater habitats: puddles, ditches, ponds, streams, lakes, and rivers, particularly waters contaminated by animal pollution or decaying organic matter (Buetow, 1968). Usually larger bodies of purer water, such as rivers, lakes, and reservoirs, have sparser populations of less common euglenoids as planktonic organisms. Marine euglenoids are more common than supposed, with Eutreptia, Eutreptiella (Figs. 6.8, 6.11(c)), and Klebsiella occurring exclusively in marine or brackish water, and many other genera having one or a few marine species. These occur in the open sea, in tidal zones among seaweeds, and as sand inhabitants on beaches. Brackish species of Euglena (Figs. 6.1, 6.2, 6.4, 6.11(a)) often color estuarine mud flats green when light intensity is low, the green color disappearing in full sunlight as the euglenoids creep away from the surface. There are also several parasitic euglenoid flagellates, mostly species of Khawkinea, Euglenamorpha, and Hegneria.

Euglenoids are characterized by chlorophylls a and b, one membrane of chloroplast endoplasmic reticulum, a mesokaryotic nucleus, flagella with fibrillar hairs in one row, no sexual reproduction, and paramylon or chrysolaminarin as the storage product in the cytoplasm.

Euglenoid cells have two basal bodies and one or two emergent flagella (Fig. 6.2). The flagella are similar to those of trypanosomes in having a paraxonemal rod (paraxial rod) that runs the length of the flagellum inside the flagellar membrane (Ngo and Bouck, 1998 ; Bastin and Gull, 1999 ; Talke and Preisfeld, 2002). The paraflagellar rod is composed of two major proteins forming an elongated alpha-helical stalk that parallels the axoneme. The one emergent flagellum in Euglena has helically arranged fibrillar hairs (no microtubules) attached along the length of the flagellar membrane. The fibrillar hairs are of two lengths: there is a single helical row of long (3 μm) hairs and two helical rows of short (1.5 μm) hairs in Euglena (Bouck et al., 1978). Other genera have flagella similar to Euglena (Hilenski and Walne, 1985). There are two basic types of flagellar movement in the class.