Vibrio parahaemolyticus is a marine bacterium recognized as the leading cause of human sea-food born gastroenteritis. V. parahaemolyticus can form two distinct cell-types: a short swimmer cell and a highly elongated swarmer cell, optimized for life in liquid and on solid surfaces, respectively. To characterize the swarming colony architecture we performed transcriptomic analysis of cells from distinct regions within the swarmer colony. We show that fully differentiated swarmer cells are present only in the peripheral swarm flares, while the center of the colony contains swimmer proficient cells with a distinct proteome. Fluorescence microscopy analyses using a double labelling reporter strain further confirmed this distinct architecture of swarm-colonies.