A conjunctive query (CQ) is semantically acyclic if it is equivalent to an acyclic one. Semantic acyclicity has been studied in the constraint-free case, and deciding whether a query enjoys this property is NP-complete. However, in case the database is subject to constraints such as tuple-generating dependencies (tgds) that can express, e.g., inclusion dependencies, or equality-generating dependencies (egds) that capture, e.g., functional dependencies, a CQ may turn out to be semantically acyclic under the constraints while not semantically acyclic in general. This opens avenues to new query optimization techniques. In this paper we initiate and develop the theory of semantic acyclicity under constraints. More precisely, we study the following natural problem: Given a CQ and a set of constraints, is the query semantically acyclic under the constraints, or, in other words, is the query equivalent to an acyclic one over all those databases that satisfy the set of constraints? We show that, contrary to what one might expect, decidability of CQ containment is a necessary but not sufficient condition for the decidability of semantic acyclicity. In particular, we show that semantic acyclicity is undecidable in the presence of full tgds (i.e., Datalog rules). In view of this fact, we focus on the main classes of tgds for which CQ containment is decidable, and do not capture the class of full tgds, namely guarded, non-recursive and sticky tgds. For these classes we show that semantic acyclicity is decidable, and its complexity coincides with the complexity of CQ containment. In the case of egds, we show that for keys over unary and binary predicates semantic acyclicity is decidable (NP-complete). We finally consider the problem of evaluating a semantically acyclic query over a database that satisfies a set of constraints; for guarded tgds and functional dependencies this problem is tractable.