They are often abundant in quiet inland waters where they may bloom in numbers sufficient to color the surface of ponds and ditches green (E. viridis) or red (E. sanguinea).

Since Euglena have features of both animals and plants, early taxonomists, working within the Linnaean two-kingdom system of biological classification, found them difficult to classify.

[7] When feeding as a heterotroph, Euglena takes in nutrients by osmotrophy, and can survive without light on a diet of organic matter, such as beef extract, peptone, acetate, ethanol or carbohydrates.

In 1674, in a letter to the Royal Society, the Dutch pioneer of microscopy Antonie van Leeuwenhoek wrote that he had collected water samples from an inland lake, in which he found "animalcules" that were "green in the middle, and before and behind white."

"[23] Twenty-two years later, John Harris published a brief series of "Microscopical Observations" reporting that he had examined "a small Drop of the Green Surface of some Puddle-Water" and found it to be "altogether composed of Animals of several Shapes and Magnitudes."

Among them, were "oval creatures whose middle part was of a Grass Green, but each end Clear and Transparent," which "would contract and dilate themselves, tumble over and over many times together, and then shoot away like Fish.

[25] In 1830, C. G. Ehrenberg renamed Müller's Cercaria Euglena viridis, and placed it, in keeping with the short-lived system of classification he invented, among the Polygastrica in the family Astasiaea: multi-stomached creatures with no alimentary canal, variable body shape but no pseudopods or lorica.

[26][27] By making use of the newly invented achromatic microscope,[28] Ehrenberg was able to see Euglena's eyespot, which he correctly identified as a "rudimentary eye" (although he reasoned, wrongly, that this meant the creature also had a nervous system).

[32] The idea of classifying the euglenoids by their manner of nourishment was finally abandoned in the 1950s, when A. Hollande published a major revision of the phylum, grouping organisms by shared structural features, such as the number and type of flagella.

[34] If any doubt remained, it was dispelled in 1994, when genetic analysis of the non-photosynthesizing euglenoid Astasia longa confirmed that this organism retains sequences of DNA inherited from an ancestor that must have had functioning chloroplasts.

[35] In 1997, a morphological and molecular study of the Euglenozoa put Euglena gracilis in close kinship with the species Khawkinea quartana, with Peranema trichophorum basal to both.

In 2015, Ellis O'Neill and Professor Rob Field have sequenced the transcriptome of Euglena gracilis, which provides information about all of the genes that the organism is actively using.

[34] Recognizing the polyphyletic nature of the genus Euglena, Marin et al. (2003) have revised it to include certain members traditionally placed in Astasia and Khawkinea.

[41] Under the aegis of Itochu, a start-up company called Euglena Co., Ltd. has completed a refinery plant in Yokohama in 2018, with a production capacity of 125 kiloliters of bio jet fuel and biodiesel per year.