Both the mitochondria and chloroplast are believed to have prokaryotic origins. They are commonly believed to once have been bacteria that were engulfed by eukaryotic cells wh … ere they lived together with a mutualistic relationship.oth the mitochondria and chloroplast are believed to have prokaryotic origins. They are commonly believed to once have been bacteria that were engulfed by eukaryotic cells wh … ere they lived together with a mutualistic relationship.