Original or unprocessed data is provided in support of the article “Label-free analysis and sorting of microalgae and cyanobacteria in microdroplets by intrinsic chlorophyll fluorescence for the identification of fast growing strain”. The data is structured into three folders named: (1) ANDOR fluorescence images and spreadsheet; (2) Fluorescence spectra for cyano and microalgae used for Figure 1A and 1B; (3) Files compling the data for Figure 2, growth curves, chlorophyl detection in droplets and micrographs of cyano in droplets