Holothurians (sea cucumbers) exist almost in all benthic marine environments and they are an important species for the commercial fisheries. In this study, the antimicrobial activity of different tissues of the sea cucumber, as a marine invertebrate, was investigated. The bacteria, Streptococcus mutans and Streptococcus sobrinus, the fungi, Candida parapsilosis, Candida albicans and Candida glabrata, were chosen for antimicrobial test, because they are opportunistic pathogens. The body wall, respiratory tree, and gastrointestinal tract of the sea cucumbers were utilized to make the extracts. Phosphate-buffered saline (PBS), ethanol (Et), and acetonitrile (ACN) were used as solvents for aqueous and organic extractions. The results showed that there were antimicrobial active compounds against infective streptococci and candid fungi. Streptococcus mutans was generally more tolerant than Streptococcus sobrinus to the sea cucumber extracts. The extracts of the respiratory tree with ACN and PBS, as solvents, showed the highest effect against Candida albicans, Candida parapsilosis and Candida glabrata. The extracts of gastrointestinal tract and the body wall with Et and PBS, respectively, had not any antifungal activity. The antimicrobial activities had been found in different extracts of the sea cucumber tissues, which could be related to the protein and non-protein compounds.