Abstract: The macronuclear and mitochondria DNA between the resting and the vegetative cell of Euplotes encysticus were comparatively analyzed by using RAPD technique in order to explore the acting feature of two genetic systems in the resting cell of ciliates. The results showed that 220 fragments were amplified in the resting and the vegetative cell DNA from Euplotes encysticus (EE) by using 35 random primers. In these fragments, both the resting and the vegetative cell macronucleus DNA had 18 and 44 specific fragments, respectively. The variance values was 28%. And 154 fragments were amplified in the resting and the vegetative cell mitochondria DNA from EE by using 32 random primers. Among them, both the resting and the vegetative cell mitochondria DNA had 19 and 25 specific fragments, respectively. The variance values was 29%. These data hinted that the structures of the macronuclear DNA in the resting and the vegetative cell of EE had some variances. The structure of both mitochondria DNA also had some variances. Therefore, in the process of EE forming resting cell, the structures of the macronuclear and mitochondria DNA all had perhaps some changes. These changes were closely related to the acute alteration for structural features and metabolism activities during the resting cell formation and related to physiological and biochemical alteration in the resting state. These results provided basic data for revealing relationship between differentiation of ciliates cell structure and acting of cell genetic substance.