This article analyzes the diachrony of the Basque marker bait-, which is a verbal prefix in subordinate clauses, but also has other functions: for example, it appears in independent clauses and indefinite pronouns. In subordinate clauses, it is used in two ways. First, it co-occurs with clause-initial conjunctions in reason, manner or result clauses or with pronouns in relative clauses. Secondly, it is used on its own, in relative, reason, result and complement clauses (with a limited group of verbs, such as emotive factive predicates or predicates of happening). The article combines evidence from a corpus study (6822 examples from 16th- to 20th-century texts) and internal reconstruction to (1) determine if and in what way the subordinator bait- and the affirmative bai ‘yes’ can be diachronically related, and (2) try to establish diachronic relations between the functions of bait-. It is proposed that the missing link between the subordinator and the affirmative particle might be a manner expression bai which had anaphoric functions. The marker bait- emerged as a reanalyzed form of the manner expression, which then gradually and through various pathways spread to different types of subordinate clauses and was reanalyzed as a subordinator.