The study present results of geobotanical investigations conducted in rice fields in the central Pamir Alai Mts (Tajikistan, Middle Asia), mainly within Syr-Daria, Pyandzh, Zeravshan, Kafirnigan, Khanaka and Surkhandaria river valleys in the years 2009–2011. The researches were focused on classification of plant communities developing within this poorly investigated area. Habitat conditions were checked including conductometry, pH reaction, temperature, depth of water and, for several plots, also soil structure. Altogether 114 phytosociological relevés using the Braun-Blanquet method were sampled. The analyses classified the vegetation into 28 communities including 24 associations. Five new plant associations and two new names for the syntaxa were proposed. The main discrimination factors for the data set are depth of water and altitude. Water reaction and conductometry have a minor role. The study shows that anthropogenic rice fields could harbour a relatively rich rush and water vegetation. Particularly extensively cultivated puddles could serve as a suitable habitat for many hygrophilous plants. We found more than 120 species in vegetation plots, including some which are rare and have not been recorded until now in this part of Middle Asia. Moreover several alien species that we found were established in rice field vegetation, e.g. Bidens frondsa or Symphyotrichum graminifolium.