Wild‐caught and pond‐reared female mud crab Scylla serrata at different stages of ovarian maturation were collected from Samar and Capiz, Philippines. Crabs were categorized into five stages according to the external morphological and microscopic appearance of the most advanced oocytes. The ovaries, hepatopancreas, muscle and newly spawned eggs (NSE) were analysed for lipid class components and fatty acids. Total lipid was higher in pond‐reared than in wild‐caught crabs but increased with ovarian maturation in both groups. Ovarian lipid peaked at the fully mature stage, coinciding with a decline in hepatopancreatic and muscle lipids. Lipid levels declined significantly in spent females. The tissues contained elevated highly unsaturated fatty acids such as arachidonic (20:4n‐6), eicosapentaenoic (20:5n‐3) and docosahexaenoic (22:6n‐3) acids, but at higher levels in late maturing and fully mature ovaries and in NSE. The type of lipid class and fatty acid components in mature ovaries as well as in NSE are generally considered to be indicative of their importance in reproductive physiology and embryonic and larval development.