This protocol aims to achieve an isotopic labeling of mixotrophic algae using 15N and 13C labeled heat-killed bacteria. It was developped to be used with the mixorophic chrysophyte Ochromonas to asses the sources of carbon and nitrogen of this algae when growing mixotrophically . Sources of nitrogen and carbon in the media used were reduced to 1 inorganic source (NH4Cl for nitrogen and bicarbonate for carbon) and 1 organic source (heat-killed bacteria); media used for Ochromonas growth was modified accordingly to reflect this.Downstream analysis of isotopic labeled Ochromonas include bulk IRMS measurements or nanoSIMS measurements.