Cyanobacteria are one of the important colonists of the soil rhizosphere. The composition of the cyanobacterial community in the rhizosphere can significantly affect the health of the soil. In this study, comparative changes in the diversity of cyanobacterial populations in abandoned rice fields chronosequences of 4 different age groups (fallow since 2, 4, 6, and 11 years) and paddy rice fields (control group) were investigated. The Shannon diversity index (Hs) was observed in the range of 1.076-2.489, which shows increased diversity with time within the chronosequence. Maximum species richness was observed in control followed by 11-year abandoned rice fields. Nostocales were found to be the most prevalent (43% 100%) and dominant order in the abandoned sites. The effectiveness of the soil parameters on the community structure of cyanobacteria and the respective dissemination of the species with them along the abandonment was determined by principal component analysis (PCA). PCA ascertained the maximum variance of organic carbon (OC) and available nitrogen (AN) in the chronosequences. Pearson’s product-moment correlations of Hs with soil OC (r = 0.947, P ˂ 0.05) and AN (r = 0.905, P ˂ 0.05) showed significant correlations. The study reveals cyanobacteria's secondary succession over time after abandonment, suggesting potential for sustainable soil reclamation methods.