The effects of salt stress on lipid composition of mature mangrove plant, Rhizophora mucronata grown in estuarine water (0.391 M Chloride ion concentration and 3020 ppm salinity) and yield of total lipids from two original protocols and four modified protocols were evaluated. It is the first approach for isolation of mangrove lipids, in which propanol treatment was used, which resulted in two fold increase in lipid yield. Rhizophora mucronata lipid composition is categorized into seven prominent classes: Polar lipids, Unknown, Sterols, Free fatty acids, Tri-terpenoids, Wax esters and Sterol esters. Comparative study of mangrove lipid profile (Rhizophora mucronata control and Rhizophora mucronata mature) with that of a salt sensitive tree Mangifera indica showed that in Rhizophora mucronata plants grown in high saline conditions, the concentration of sterol esters, wax esters and sterols get decreased and tri-terpenoids, free fatty acids, unknown lipids and polar lipids get increased.