Evaluation of habitat fragmentation and connectivity between habitats is one　of the most important issues in landscape ecology. There were only few case studies for amphibians which treat this issue in fine scale of landscape, such as several square kilometers. For highly accurate and efficient evaluation of habitat fragmentation in fine scale, population genetic approaches will be needed. In the present study, we evaluated the habitat fragmentation of Japanese brown frogs (Rana japonica) by using population genetics in the study site (approximately 3 x 3 kilometers) at Inba area, Chiba prefecture. Japanese brown frog is one of the locally decreasing species, and suitable model animal for such analyses because their population is considered to form a meta-population. We used D-loop region of mitochondrial DNA (mtDNA) and 8 micro-satellite (MS) regions as genetic markers for calculating Fst as genetic distance among populations. Fst was compared with geological distances and locations of breeding sites by using Barrier and SAMOVA to detect barriers of gene flow. We also estimated gene flow itself by using Bayes-ASS analysis from MS. We found three genetic groups from the results of mtDNA analyses, but the results from the MS showed a bit different figures. We will discuss the difference of two analyses and the reasons of the differences.