Symbiont-bearing benthic foraminifera host multiple types of endosymbiotic algae. Provided that the symbiont diversity is functionally relevant, the different type of symbiont could provide the host an adaptive flexibility in changing environment. Here we investigate the eukaryotic microbiome flexibility of two species of benthic foraminifera, Amphistegina lobifera and Pararotalia calcariformata which are two recent invaders of the eastern Mediterranean sea. We exposed the two species to thermal stress, measured their photosynthetic efficiency and analyzed the taxonomic composition of their microbiome using illumina sequencing of the eukaryotic V4.