Hydrophilic benzo[b] thiophene metabolites produced by Rhodococcus sp. strain T09 were isolated by a solid-phase extraction and a derivatization method, which prevented the dehydration that often occurs during liquid-liquid extraction (LLE), and were identified by GC with atomic emission detection and GC-MS. As a result, cis- or trans-2-(2'-hydroxyphenyl) ethen-1-ol, previously reported as the tautomer 2-(2'-hydroxyphenyl) ethan-1 al, and 2-(2'-hydroxyphenyl) ethen-1-sulfenic acid and its isomer, 1-(1'-hydroxyethenyl) benzene-2-sulfenic acid, were identified. Benzothiophene desulfurization in culture broth at neutral pH by the strain T09 was modified as a branched metabolism from benzothiophene S-oxide based on the above compounds.