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The consequences of climate change and land subsidence are often related to sea level rise/fall. Mangrove extinction and migration were assessed through palynological studies in two sedimentary cores in order to address climate, Relative Sea level (RSL) and its relation to geomorphology since 8420 cal. yr BP from Kanuru (500 cm deep) and since 5850 cal. yr BP from Machilipatnam (118 cm deep), Krishna delta, India. Four units/nine phases of sediment depositional environment were identified on the basis of marine/terrestrial palynomorphs. In Unit 1, the marine palynomorphs indicate palaeoshoreline in Kanuru from 8420 to 8300 cal. yr BP which is now ~4–5 km from the present-day shoreline, but after a short span a retreat in sea level took place between 8300 and 7040 cal. yr BP. About three to four short-term intermittent rise/fall in RSL were recorded in Unit 2 between 7040 and 3980 cal. yr BP in Kanuru and between 5225 and 3240 cal. yr BP in Machilipatnam. During this period, the diversity of mangroves was more in Machilipatnam and only salt-tolerant mangroves were present in Kanuru. Unit 3 is characterized by non-estuarine sediment deposition since 3920–240 cal. yr BP in Kanuru and since 3240–950 cal. yr BP in Machilipatnam. Unit 4 shows a rise in RSL in both the studied sites which began much earlier in Machilipatnam than in Kanuru. Loss of mangrove diversity and dominance of salt-tolerant mangroves were recorded in Unit 4. Results indicate climate-induced RSL fluctuations highlighting the cooling event of 8.2 ka BP from Kanuru site and duration of intermittent rise/fall of RSL during middle Holocene transgression. The rate of sea level rise during the period was not continuous but interrupted by three to four retreats. At present, the evidence of these are at different depths in both the sites and in other contemporary sites along the east coast of India, suggesting neo-tectonics in the vertical stack of Holocene sediment. The geomorphology of the studied sector is tectonically controlled which may increase deltaic instability in future.