Organelles have their own genomes. When chloroplast DNA is sequenced and compared to genomes from members of the cyanobacteria, the sequence is nested within cyanobacteria. This is strong evidence for the hypothesis that:

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The fact that chloroplast DNA is nested within cyanobacteria strongly supports the endosymbiotic theory, which states that chloroplasts originated from a symbiotic cyanobacterium that was incorporated into a host cell and evolved into a permanent organelle. This theory also explains why chloroplasts have their own genomes separate from the nuclear genome of the cell they reside in.

Organelles Have Their Own Genomes