Mangroves are used by folklore in indigenous medicine for the treatment of diseases. They contain an array of pharmacologically significant bioactive compounds. The endophytes of the mangroves have the capability of producing biologically active compounds which may be similar to their host plant. They are also able to produce novel and unique bioactive compounds which can be used in therapeutics. Bacillus and Streptomyces are the major genera of bacterial endophytes found in the mangroves. The major groups of bioactive compounds produced by the bacterial endophytes of mangroves include terpenoids, alkaloids, polyketides, etc. The bioactive compounds produced by the endophytes possesses biological activities, such as antibacterial, cytotoxic, antioxidant activity, etc. These compounds have profound applications in the discovery of drugs. The present chapter focuses on the bacterial endophytes found in the mangroves, the bioactive molecules produced by them, and the pharmacological activities associated with these endophytes.