The regioselective catalytic hydrogenation of benzo[b]thiophene (BT) and quinoline (Q) were carried out in a biphasic (water/decalin) medium using two ruthenium(II) complexes as catalyst precursors. These water soluble complexes were of the type RuHCl(TPPTS) 2(L) 2, (where L=1,2,3,4-tetrahydroquinoline [THQ], 1, or Aniline [An], 2). The catalytic results from these precursors were compared with their analogue derivates from TPPMS ( meta-sulfonato-phenyldiphenylphosphine in its sodium salt form) RuHCl(TPPMS) 2(L) 2 (L=THQ, 3 and An, 4). In the biphasic hydrogenation of BT, the type of nitrogen donor ligand, as well as the type of phosphine, has an influence on the catalytic activity. This effect was not observed during the hydrogenation of quinoline. The only products detected during the hydrogenation of BT and Q were 2,3-dihydrobenzo[b]thiophene (DHBT) and 1,2,3,4-tetrahydroquinoline (THQ), respectively. No evidence of CS or CN bond cleavage were detected. In all the reactions, the catalyst precursors remained in the aqueous phase.