Yes, extra genomic DNA is present in both prokaryotes and eukaryotes.In case of eukaryotes, extra genomic DNA is present in two organelles, e.g., Plastids and mitochondria. Both these organelles with the help of their own DNA, synthesise some of their proteins. Thus, these organelles are known as semiautonomous organelles.
In case of prokaryotic cells, the extragenomic DNA is present in the form of plasmids. The plasmids are circular DNA molecules, which confer certain unique phenotypic characters to such bacteria. One such character is resistance to bacteria. This plasmid DNA is also used to monitor bacteria transformation with foreign DNA.