Weeds are major biotic constraints to rice production worldwide. Compared to other sub-regions, weed communities of rice are not well described for East Africa and there is limited information on environmental factors affecting the distribution of species. This study aimed to address these knowledge gaps. Seasonally flooded rice production fields of 31 sites in Rwanda, Tanzania, Kenya and Uganda, across three altitude classes (Low: <200 m; Medium 200–1,000 m; High: >1,000 m), were surveyed for weed species using quadrats. Data analyses involved multivariate approaches, non-parametric Kruskal–Wallis tests and logistic regressions, followed by calculation of ranked species abundance and Shannon Wiener Index diversity analyses. A total of 286 weed species, belonging to 59 families, were recorded with 42 species not previously reported as lowland rice weed in the sub-region. Twenty-four species were identified as abundant across altitudes. Weed species diversity was higher at medium altitudes compared to high and low altitudes. Significant patterns of floristic distinction between altitudinal classes were observed, with 80% of dissimilarity. The high altitude was dominated by Echinochloa colona, Leptochloa squarrosa and Sphaeranthus suaveolens, the medium altitude was dominated by Crassula granvikii, Pycreus lanceolatus and Ageratum conyzoides while the low altitude was dominated by E. colona, Cyperus difformis and Cyperus esculentus. The weed species composition of seasonally flooded rice fields in East Africa is diverse. Identification of a limited group of (24) commonly abundant weed species as well as the articulation of altitude-specific weed species groups will facilitate the development of better tailored weed control programmes.