We describe a Markov chain method for sampling from the distribution of the hidden state sequence in a non-linear dynamical system, given a sequence of observations. This method updates all states in the sequence simultaneously using an embedded Hidden Markov Model (HMM). An update begins with the creation of "pools" of candidate states at each time. We then define an embedded HMM whose states are indexes within these pools. Using a forward-backward dynamic programming algo- rithm, we can efficiently choose a state sequence with the appropriate probabilities from the exponentially large number of state sequences that pass through states in these pools.