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Abstract We use graph theory simulations and single molecule experiments to investigate percolation properties of kinetoplasts, the topologically linked mitochondrial DNA from trypanosome parasites. The edges of some kinetoplast networks contain a fiber of redundantly catenated DNA loops, but previous investigations of kinetoplast topology did not take this into account. Our graph simulations track the size of connected components in lattices as nodes are removed, analogous to the removal of minicircles from kinetoplasts. We find that when the edge loop is taken into account, the largest component after the network de‐percolates is a remnant of the edge loop, before it undergoes a second percolation transition and breaks apart. This implies that stochastically removing minicircles from kinetoplast DNA would isolate large polycatenanes, which is observed in experiments that use photonicking to stochastically destroy kinetoplasts fromCrithidia fasciculata. Our results imply kinetoplasts may be used as a source of linear polycatenanes for future experiments.