Abstract. We solve the twisted conjugacy problem on Thompson's group F . We also exhibit orbit undecidable subgroups of Aut(F ), and give a proof that Aut(F ) and Aut + (F ) are orbit decidable provided a certain conjecture on Thompson's group T is true. By using general criteria introduced by Bogopolski, Martino and Ventura in [5], we construct a family of free extensions of F where the conjugacy problem is unsolvable. As a byproduct of our techniques, we give a new proof of a result of showing that F has property R∞, and which can be extended to show that Thompson's group T also has property R∞.