In this letter, the problem of estimating the physical layer (PL) scrambling code sequence of DVB-S2 is studied. We present the first ever scheme to estimate the scrambling sequence. The scheme is based on hypothesis testing. By analyzing the PL scrambling process, we construct a new sequence equivalent to the scrambling sequence. We then use hypothesis testing to estimate the new sequence. The threshold for the hypothesis testing is also discussed. The experiment results show that the performance of our estimation scheme can work even under high BER.