The global marine environment is highly heterogeneous although the nature of heterogeneity can vary spatially. In this study, the nature and extent of spatial heterogeneity of the coastal, marine ecoregions along the Central-Eastern and South-Eastern coast of India (parts of Andhra Pradesh, Pondicherry and Tamil Nadu) was studied, which represent two different – Central-Eastern, and South-Eastern – coastal ecoregions. Several environmental (e.g., salinity, temperature, and nutrients of the ocean water, etc.) and physical (e.g., substrate type, energy condition of the coast) parameters were measured (quantitative as well as semi-quantitative approach) and analysed by using several bivariate and multivariate methods. Our results clearly point out that the Central-Eastern, and South-Eastern marine, coastal ecoregions of India are highly heterogeneous among themselves, and even smaller ecoregions (i.e., sub-ecoregions) within each of these larger ecoregions are also different from each other. Thus, each of these ecoregions is internally highly heterogeneous. In addition, there is no consistent spatio-latitudinal change in the environmental variables along the eastern coast of India. © 2020, Indian Academy of Sciences.