A method of extracting fucoidan from a biological material is provided. The method comprises (a) combining a biological material containing fucoidan and a medium to form a mixture; (b) applying ultrasonic waves to the mixture while the mixture is at a temperature of less than about 60 C; (c) extracting fucoidan into the medium from the biological material to produce a fucoidan containing solution and insoluble biological matter; and (d) separating the fucoidan containing solution from the insoluble biological matter to obtain a fucoidan containing extract. Methods of using the fucoidan containing extract and pharmaceutical preparations containing the fucoidan containing extract are also provided.