The basic difference between the nuclear DNA and the mitochondrial DNA is that the nuclear DNA is linear in shape while the circular DNA is present in the mitochondria. Apart … from this, the mode of replication also differs in both of them.onfidence votes 68. Nuclear DNA, which is found in the nucleus, is inherited from both parents. On the other hand, mtDNA is found in the mitochondria and, in most multicellular organisms, is inherited from the maternal lineage.