Wild mud crabs of the genus, Scylla paramamosain were acclimatized in tanks in the AKUATROP hatchery. Eye stalk ablation was applied on the mud crabs before transferring them into a recirculating aquaculture system, where they were fed marine fish, squid and cockles for a period of one month until they produced eggs. The larvae which hatched out were placed in different larval tanks with continuous aeration. Larvae were fed daily with artemia. The density of larvae culture was 100-300 individuals per liter. The peritrich ciliates found on megalopa larva of mud crabs, Scylla paramamosain were Zoothamnium alrashedi and Myoschiston duplicatum and an unidentified peritrich ciliate. Mangrove leaf extract of Rhizophora apiculata showed that it is capable of being an antiprotozoan product as the zooids of the peritrich ciliates dropped off after treatment with the extract. The breeding tanks were kept clean, probiotics was introduced with plenty of aeration. Green water system was activated to ensure plenty of natural food namely rotifers to ensure moulting of megalopa larva into crablet larva.