Microalgae　are　a　commercially　viable　route　for　the　production　of　carotenoids.　Chlorella　sp.　BR2　was　treated　with　plant　hormones　indole-3-acetic　acid,　salicylic　acid,　abscisic　acid　and　methyl　jasmonate　and　screened　for　enhanced　carotenoid　production.　Indole-3-acetic　acid　was　the　only　hormone　with　an　inductive　effect　on　carotenoid　accumulation.　As　such,　transcriptome-wide　changes　following　auxin　treatment　were　profiled　using　RNA-Seq　and　expressed　sequences　reconstructed　with　de　novo　assembly.　This　revealed　the　active　pathway　components　of　auxin-induced　carotenogenesis.　Data　analysis　specified　the　differentially　expressed　genes　involved　in　auxin　biosynthesis　and　signal　transduction,　which　hint　at　close,　yet　unique　relationship　to　equivalent　pathways　in　higher　plants.　Unlike　in　plants,　the　ancient　ABP1/SCFSKP2A/IBR5-mediated　pathways　for　auxin　response　likely　acted　as　the　primary　signaling　route　in　Chlorella.　As　carotenoids　are　precursors　for　abscisic　acid　and　antagonists　of　reactive　oxygen　species,　the　findings　suggest　a　potential　link　between　auxin　signaling　and　abiotic　stress　tolerance.