Though is native, from Old English þeah, partly reinforced by Old Norse þo — the same word arriving from both sides of a bilingual population. Both go back to the Germanic demonstrative that also gives that and the.
Its interest is entirely in the -ough. That spelling covers a rasping consonant that English inherited and then disposed of in several different ways depending on the word and the dialect: silent in though and through, an f in enough, rough and tough, and something else again in plough and thorough. Etymonline notes that though did not follow laugh and tough into the f, although a tendency to end it that way existed between about 1300 and 1750 and survives in dialects. Seven spellings, one letter sequence, no rule — which is why -ough is the standing joke of English orthography.
though (adv., conj.) c. 1200, "notwithstanding that, conceding or allowing that," introducing a clause, used in contrasting or in correlation, from Old English þeah , þeh "though, although, even if, however, nevertheless, still, yet;" and in part from Old Norse þo "though," both from Proto-Germanic *thaukh (source also of Gothic þauh , Old Frisian thach , Middle Dutch, Dutch doch , Old High German doh , German doch ), from PIE demonstrative pronoun *to- (see that ). The evolution of the terminal sound did not follow laugh , tough , etc., though a tendency to end the word in "f" existed c. 1300-1750 and persists in dialects. also from c. 1200