Abstract: Carchesium polypinum, a cosmopolitan protozoa, belongs to Carchesium Ehrenberg, Peritrichida Stein, Oligohymenophorea de Puytorac et al., Ciliophora Doffein. From the 1940s, many wide and deep resesrches of its morphology and structure have been done at organism, subcellular and molecular levels. Karl described detailed characteristics of the whole organism first in 1932. After that, Lom studied the accurate fiber structure under pellicle, which is the most important criterion of speices identification and analysis of relationship between populations of ciliate. Along with the development of the molecular techniques, there are some reports about the protein and DNA structure of it, but the knowledge of isozyme--the important technique studies about species identification, relationship of intraspecific and interspecific and population genetic structure of this protozoa is very poor. In this paper, polyacrylamide gel electrophorosis was used to study four isozymes-Esterase (EST), Malate dehydrogenase (MDH), Lactate dehydrogenase (LDH) and Acid phosphatase (ACP), of three Carchesium polypinum populations from the Sand Lake of Wuhan, Hubei province. The results show that EST can be divided into 7 brown bands and 6 purple bands and are controlled by six loci (Est-1-Est-6), out of which Est-1, Est-2,Est-3 and Est-5 are heterozygotes and Est-4 and Est-6 are homozygotes. The analysis of its electrophoretic banding patterns indicates that its quaternary structure involves 2 patterns: monomer and dimmer. The bands of MDH are coded by five loci (Mdh-1-Mdh-5), in which Mdh-1, Mdh-4 and Mdh-5 are heterozygotes and Mdh-2 and Mdh-3 are homozygotes. These bands can be distinctly divided into two typical kinds-s-MDH bands and m-MDH bands. The LDH expressed in Carchesium polypinum is more than it dose in other protozoans. Five bands are coded by one heteozygotic locus-AB, compared with the conditions in higher animal. ACP has only one band and is controlled by a homozygote locus. This work can not only accumulates the information of isozymic characters of wild Carchesium polypinum, but also provide a powerful lever for the studies on the population genetics and ecology.