Ammonia oxidizing bacteria (AOB) are important microorganisms in rice paddy field ecosystems because they play a key role in the nitrogen (N) cycle by converting ammonia (NH3) to nitrite (). In this study, we investigated AOB associated with three types of weeds in a Japanese paddy field (semi-aquatic Echinochloa oryzicola Vasing, floating Lemna paucicostata Hegelm and submerged Najas graminea Delile) using molecular techniques polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and DNA sequencing targeting ammonia monooxygenase (amoA) gene. This work confirmed that rice paddy weeds harbor AOB and that the community composition is different for each type of weed. However, all AOB sequences associated with the tested weeds were closely related to known species of Nitrosospira-like AOB isolated from soil, suggesting that AOB associated with weeds were not specific to weeds and can also be found in the soil. Nitosomanas-like AOB were not detected on any of the weeds tested. In addition, the most dominant AOB strains present in the tested weeds were closely related to Nitrosospira sp. Ka3 and Nitrosospira sp. CT2F. The phylogenetic tree revealed that most of the AOB detected in the present study belonged to amoA cluster 1.