© 2017, © 2017 The Journal of Horticultural Science & Biotechnology Trust. The use of microbubbles (MB) can improve the oxygen supply to plants grown under the deep flow technique of hydroponic culture. In a previous study, we compared the growth of komatsuna (Brassica rapa L. perviridis, Japanese mustard spinach) plants grown under hydroponic culture with MB generated by the pressurisation (P) method and the gas-water circulation (G) method. Plant growth was significantly lower in the presence of the P-MB than the G-MB. In this study, we aimed to identify the factor(s) responsible for the poor growth of komatsuna plants in the presence of P-MB. At three weeks after planting, the growth of the P-MB plants was less than the growth of G-MP plants and controls, regardless of dissolved oxygen concentrations. Analysis of the root tips by transmission electron microscopy showed plasmolysis of the P-MB root tip cells but not of the G-MB and control root tips. Our results suggest that the growth inhibition of plants grown in the presence of P-MB is due to inhibition of water and nutrition absorption from root tip cells due to this plasmolysis. This is likely due to oxidisation of root tip cells by hydroxyl radicals generated by many fine MB and/or osmotic stresses caused by the MB.