After 1970 s, a lot of wetland sites have been excavated in Japan. But there are several problems in the excavations of wetland sites. In this paper, I discussed about two problems: stratigraphy and synthetic interpretations of the excavation data. The first, it is important to recognize the difference of paloesols(paleo soils) from sediments, and the relation between structural remains and paleosols. The second, it is necessary to consider taphonomy of plant fossils, and understand the relation between archaeological records and the data of plant fossils in the stratigraphy. I introduced about the case studies of Uriudo, Ikejima-Fukumanji, Shiki and Tainaka site on Kawachi plain as the examples of excavation of the wetland sites in Japan.