Abstract: Genes in the germline (micronuclear) genome of protozoan ciliates are interrupted by multiple, non-coding sequences called internal eliminated segments (IESs) and macronuclear destined segments (MDSs). In the micronucleus, the MDSs are not arranged sequentially but scrambled for some genes. Studying scrambled gene structures will provide a better understanding of the molecular mechanisms of its evolution. In this study, we compared the complete macronuclear gene sequences and complete/incomplete micronuclear gene sequences of Actin I, α-telomere-binding protein (α-TBP), and DNA polymerase α (DNA pol α) of Oxytricha species (Oxytricha sp. (ZJ)) collected from water samples of Huguang mangrove in Zhanjiang with those of other Oxytricha species, and had 3 major findings. The scrambled patterns of the micronuclear Actin I gene in O. sp. (ZJ) were similar with those of O. nova, but shown significant differences with other species in genus Oxytricha. We revealed that the shifts of MDS-IES junctions between scrambled MDSs are not more conservative than those between non-scrambled MDSs, which is inconsistent with a previous study. The scrambled pattern of micronuclear α-TBP gene in O. sp. (ZJ) is same with that of O. nova, and the lengths of their IESs of these two species are also similar. The scrambled pattern of micronuclear DNA pol α gene in O. sp. (ZJ) is different from any of the previously reported species, and it is only somewhat similar to O. trifallax. Moreover, an IES transited to MDS was observed in DNA pol α gene, which caused the missing of its original MDS.