In this paper the problem of distributed source coding (DSC) of binary sources with side information at the decoder is addressed. A scheme is proposed based on Raptor codes which are a new class of rateless codes. The decoding scheme is adapted to this problem by implementing a message passing strategy between the constituent decoders of Raptor codes at each decoding iteration. The general case in which the sources are modeled as hidden Markov processes (HMPs) is considered. To exploit the Markovian nature of the sources, a module is added to the decoder to help the estimation process. This module is necessary to achieve good performance.