There are various ways because of which the genetic material of Prokaryotes and Eukaryotes differ with each other. The most obvious difference is that the DNA of prokaryotes is arranged in circular structures while that of eukaryotes is arranged in linear strands. Secondly, eukaryotes genome has multiple chrmosomes while prokaryotes genome has single chrmosomes. Thirdly, prokaryotes DNA is the fraction of length of nucleic acid strand while that of eukaryotes is lenghty and complex. The fourth difference is that coding sequence in prokaryotic genome is 90% as compare to 3% in eykaryotic genome. Another difference is that Eyokaryotes have more DNA as compare to Prokaryotes. There are a number of other differences as well and get more details from the given link:
Difference in Genetic Material
Difference in Genetic Material
