Rice is one of the most economically important cereal crops in the world. The genus Echinochloa is the most competitive and difficult to control weeds in the rice fields. Improving the knowledge on the genetic diversity and structure of Echinochloa spp. can supply crucial information for designing effective management strategies for weed control in rice breeding. In the study, 28 Echinochloa spp. genotypes were subjected to the analysis of genetic diversity using four amplified fragment length polymorphism selective primer combinations. The number of polymorphic fragments per primer combination detected ranged from 28 to 50 bands with an average of 41.5 bands. Average polymorphic information content (PIC) was 0.26 in overall primer combinations. E-ACA-M-CAG primer combination showed the highest PIC (0.52) which can be a good candidate primer combination to verify genetic diversity in Echinochloa spp. The unweighted pair-group method of the arithmetic average and principal coordinate analysis showed a clear distinction among the genotypes and the genotypes divided into three clusters in the dendrogram results. A model-based structure analysis revealed the presence of two populations. The accessions were clearly assigned to a single population in which > 70 % of their inferred ancestry was derived from one of the model-based populations. However, three genotypes (10.7 %) in the sample were categorized as having admixed ancestry. The study showed that genetic variation and population structure are determined among genotypes collected from different locations. High level of genetic variation in both intra and inter species was detected.