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The partitioning of water and tetramethylrhodamine-conjugated-10-residue oligopeptides from the aqueous phase of microdroplets into Span 80 reverse micelles was observed by utilizing microdroplet arrays. Each peptide was dissolved in phosphate buffer saline, and initially encapsulated in arrayed droplets. An organic phase containing the reverse micelles was added to the microdroplets. Here, the hydration degree of the reverse micelle was adjusted by contact of the organic phase with a 1.0 M NaCl aqueous solution or with a phosphate buffer saline before combining it with the microdroplets. For micelles treated with a 1.0 M NaCl, significant water transport from the microdroplet to the micelle was observed, and peptide with low solubility in water was transported to the reverse micelles, while those with high solubility in water were not. For micelles treated with phosphate buffer saline, the water transport was minimal, and no significant peptide transport was observed. These results suggest that the partitioning of low-solubility oligopeptides requires accompanying water transport to the reverse micelle phase.