Echinochloa crus-galli is a serious weed in rice crop ecosystems, and widely distributed in all climatic zones of Sri Lanka. Its management was challenging through the efforts made for decades. Global scientific evidence show presence of multiple biotypes and a Sri Lankan study explained the presence of two Echinochloa crus-galli biotypes, where one has strong resistance over most of the available grass killer herbicides, however, the gentic nature of populations were not studied thereafter. Regardless the various combinations of management options studied the efforts were fruitless as the Echinochloa populations thrive well in the rice fields. In addition to E. crus-galli there are four other species namely E. colona, E. frumentacea, E. glabrescens, and E. stagnina available in Sri Lanka. Except for E. frumentacea all others are reportedly serious weeds and for E. frumentacea which is introduced to the nothern part of the country a long term back , the status is still unknown. Further the similarities in the morphology among the species, made them difficult to differentiate without a proper competency in taxonomic identification thereby, these species may also present in the rice fields and misidentified as E. crus-galli. The un-noticed biotypes and incorrectly identified species may have subjected to the management options designed for an early population of E- crus-galli, which might be the reason for its poor management regardless the efforts. This study was aimed at developing genome-wide SSR markers in-silico, for E. crus-galli and was planned to utilize them in studying genetic variability of the different populations. GMATA v. 2.3 was used to identify 201,846 different SSR loci. A total of 196,616 unique primer pairs were generated targeting their amplification. Primer pairs that could amplify up to  five genomic regions were extracted eliminating others to retain 50,307 pairs (100,614 primers). Each primer was then manually analysed for tthe following. Primers with GC content (>60%) and for melting temperature ranging between 55-65OC were selected and others were eliminated. The ability generating and the relative stability of the selected primers to form secondary structures such as hairpin structures, self-dimers and hetero dimers were analysed to remove them from downstream analyses. Further, the mismatches in melting temperatures were also examined. A tota, of 316 primers were retained and used in e-PCR to validate their ability in amplification of the selected SSRs with available gene pools of five Echinochloa species (collected from various genome databases) present in Sri Lanka. After successful amplification results generated from e-PCR, 50 randomly selected SSR markers were produced through a commsercial supplier and was used in amplifying related genomic regions of 107 different Echinochloa leaf samples collected from diverse localities and populations. The specimens from five different species was used to understand the cross ransferability of the markers, while E. crus-galli samples were utilised in studying the population variations. Based on the results, the selected primers are found to have successful in differntiating different species while a considerable population variations were detected.