Shannon and Simpson indexes are used for species diversity analysis of ecosystem. In species diversity analysis of ecosystem, not only frequency of each species but also survey size have to be considered. In this study, total information composed with knowledge and ignorance was suggested as a species diversity analysis method for ecosystem survey. To apply developed method, flora in the Sangachun river valley was sampled with 19 sites and 198 species. In applying results, Shannon index shows more reasonable results than Simpson index by the variance of sample size but has difficulties of determining the relation of surveying species number and sample site number. Suggested total information can overcome this difficulty by the relation of knowledge and ignorance.