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Abstract--The road towards a single internal electricity market in Europe is hampered by limited cross-border transmission capacity. As investing in new cross-border transmission capacity is a long term process with a lot of challenges, optimal use of the existing capacity is the best short term measure. In Europe, Flow-based Market Coupling (FMC) is the state of the art methodology in this regard and is near its implementation in the Central and Western Europe (CWE) region. The CWE transmission system is equipped with power flow controlling devices (PFCs), such as Phase Shifting Transformers (PST), to mitigate loop flows. Such devices can change the flow pattern throughout the system and therefore affect the FMC output. This paper analyzes the potential influence of PSTs in the results of FMC. The FMC algorithm is modified adding PST setting as a variable and illustrated for a 3-zone example. The main objective of the proposed algorithm is to include the PST settings in the search for optimal cross-border transmission capacity allocation. Index Terms-- Market coupling, Phase shifting transformers