Microbes are the most abundant and evolutionarily diverse organisms in the biosphere, and have unparalleled importance for the health of our planet. They represent 50-90% of total ocean biomass, regulate ocean chemistry by driving biogeochemical cycles and influence climate. To date, microbial ecologists have had limited opportunity to carry out functional analyses on living micro-organisms immediately after sampling from their natural habitats in field locations. This is because of limited access to robust, ocean-going analytical technologies. Here we report on the abundance and physiology of microbes sampled in the southwestern Pacific Ocean during two ocean voyages. On board experiments were designed to assess the tolerance of upper ocean microbes to changes in temperature. Fluorescent markers targeting cell wall properties and intracellular reactive oxygen, as well as intrinsic photosynthetic pigments were quantified using an Influx mariner flow cytometer. Analyses demonstrated populations of marine microbes have varying tolerance to temperature change, and use divergent physiological strategies to cope with thermal stress. The implications of what this means for overall marine ecosystem function in light of a warming climate will be discussed.