Casuarina spp. are major windbreak species in coastal forests of Taiwan. With great ability for rapid growth and adaptability to adverse environmental conditions, they enhance soil stabilization and provide protection and rehabilitation for coastal areas. Many factors may limit the reproduction of Casuarina in coastal areas such as infertile soil, drought, salt stress, litterfall, and weeds. In addition, nitrogen is generally considered one of the major nutrients in plant growth, and Casuarina plants can obtain nitrogen sources through association with Frankia via root nodules. In order to understand the interaction between diverse diazotrophic diversity and different test sites of Casuarina spp. determine whether it is the diversity level of diazotrophic on healthy and on declining Casuarina spp., or the number of nitrogen-fixing bacteria in the nodules of Casuarina spp., direct amplification of the nifH gene for a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis with the primer pair polF-GC/polR was applied in this study. The results demonstrated that there were 2 groups of nitrogen-fixing bacteria collected from these root nodule samples that appeared on the PCR-DGGE profiles. Whether Casuarina stands are on the decline or not, a high diversity of diazotrophic community has been observed among all test sites.Therefore, this study shows that the declining Casuarina is not related to the diazotophic diversity.