The generation of air microbubbles in microfluidic systems or in capillaries could be of great interest for transportation (single cell analysis, organite transportation) or for liquid compartmentation. The physicochemical characterization of air bubbles and a better understanding of the process leading to bubble generation during electrophoresis is also interesting in a theoretical point of view. In this work, the generation of microbubbles on hydrophobic Glaco TM coated capillaries has been studied in water-based electrolyte. Air bubbles were generated at the detection window and the required experimental parameters for microbubbles generation have been identified. Generated bubbles migrated against the electroosmotic flow, as would do strongly negatively charged solutes, under constant electric field. They have been characterized in terms of dimensions, electrophoretic mobility, and apparent charge.