The indiscernibility relation is the basic concept in Rough set theory, a novel representation of indiscernibility relation using Zero-Suppressed BDDs is proposed in this paper. Through introducing the indiscernibility matrix and the indiscernibility graph, we put forward the encoding of the variable and give the characteristic function. Once the characteristic function is constructed, it can be represented using ZBDDs.And further, combined with an example, we analyze the effectiveness of this method. It provides a basis for deal with rough set computing.