Flavin-dependent halogenases require FADH2 , O2 and halide salts to halogenate their substrates. We describe crystal structures of the tryptophan 6-halogenase Thal in complex with FAD or with both tryptophan and FAD. If tryptophan and FAD were soaked simultaneously both ligands showed impaired binding and in some cases only the AMP or the adenosine moiety of FAD was resolved, suggesting that tryptophan binding mainly increases mobility of the FMN moiety. This confirms a negative cooperativity between substrate and cofactor binding previously described for other tryptophan halogenases. Binding of substrate to tryptophan halogenases reduces the affinity for the oxidized cofactor FAD presumably to facilitate regeneration of FADH2 by flavin reductases. This article is protected by copyright. All rights reserved. © 2019 The Protein Society.