There has been a longstanding expectation that the optical resolution embodiment of photoacoustic tomography could have a substantial impact on gastrointestinal endoscopy by enabling microscopic visualization of the vasculature based on the endogenous contrast mechanism. Although multiple studies have demonstrated the in vivo imaging capability of a developed imaging device over the last decade, the implementation of such an endoscopic system that can be applied immediately when necessary via the instrument channel of a video endoscope has been a challenge. In this study, we developed a 3.38 mm diameter catheter based, integrated optical resolution photoacoustic and ultrasonic miniprobe system and successfully demonstrated its intrainstrument channel workability for the standard 3.7 mm diameter instrument channel of a clinical video endoscope based on a swine model. Through the instrument channel, we acquired the first in vivo photoacoustic and ultrasonic dual mode endoscopic images from the esophagogastric junction, which is one of the most frequently cited anatomical sites in the gastrointestinal tract in relation to Barretts esophagus. Moreover, from a rat colorectum in vivo imaging experiment, we visualized hierarchically developed mesh like capillary networks with a hole size as small as 50 microns, which suggests the potential level of image details that could be photoacoustically provided in clinical settings in the future.