word-forming element meaning "under, beneath; behind; from under; resulting from further division," from Latin preposition sub "under, below, beneath, at the foot of," also "close to, up to, towards;" of time, "within, during;" figuratively "subject to, in the power of;" also "a little, somewhat" (as in sub-horridus "somewhat rough"), from PIE *(s)up- (perhaps representing *ex-upo-), a variant form of the root *upo "under," also "up from under." The Latin word also was used as a prefix and in various combinations.
In Latin assimilated to following -c-, -f-, -g-, -p-, and often -r- and -m-. In Old French the prefix appears in the full Latin form only "in learned adoptions of old Latin compounds" [OED], and in popular use it was represented by sous-, sou-; as in French souvenir from Latin subvenire, souscrire (Old French souzescrire) from subscribere, etc.
The original meaning is now obscured in many words from Latin (suggest, suspect, subject, etc.). The prefix is active in Modern English, sometimes meaning "subordinate" (as in subcontractor); "inferior" (17c., as in subhuman); "smaller" (18c.); "a part or division of" (c. 1800, as in subcontinent).
species n.
late 14c., in logic, "a of individuals or things," from Latin species "a particular sort, kind, or type" (opposed to genus), originally "a sight, look, view; outward appearance, shape, form," a derivative of specere "to look at, to see, behold" (from PIE root *spek- "to observe"). In English it is attested from 1550s as "appearance, outward form."
Latin species "a sight; outward appearance" had many extended senses, including "a spectacle; a mental appearance, an idea or notion;" also "semblance, pretext; manner, fashion; display, beauty; a likeness or statue; reputation, honor." Typically it was used in passive senses. Also compare spice (n.).
In Late Latin, in logic and legal language, it acquired the meaning "a special case," especially (as a translation of Greek eidos) "a included under a higher class; a kind; a sort; a number of individuals having common characteristics peculiar to them." The notion (as Lewis & Short puts it) is "The particular thing among many to which the looks are turned."
The English word is attested from 1560s as "a distinct (of something) based on common characteristics." The specific use in biological sciences in reference to groups of living things recognizably distinct from all others by their inherited characteristics is from c. 1600. Endangered species is attested by 1964.