We developed phase-control pulsed force mode (p-PFM) as the operation mode for atomic force microscopy (AFM). The p-PFM allowed us to observe soft or weakly adsorbed materials in a liquid environment using a conventional AFM apparatus, and allowed for force curve mapping (FCM) after offline data processing. We applied the p-PFM to a rhodium-octaethylporphyrin (RhOEP) layer on highly oriented pyrolytic graphite (HOPG), which is applicable to anode catalysts of fuel cells. The RhOEP/HOPG system was stably observed in water by this mode. In the p-PFM image, we found both large and small protrusions, which were not observed in the dynamic force mode, in air. The detailed force analysis suggested that these protrusions are nanobubbles located on the HOPG substrate exposed in holes or pits of the RhOEP layer. (C) 2014 Elsevier B.V. All rights reserved.