| Genetic map | Physical map |
| It is the calculated map distance based on the crossover percent between two linked genes | The actual physical distance between linked genes |
| This map distance highly varies as the frequency of crossing over varies in a different segment of chromosomes and it is only a predicted value | The physical distance of linked genes bears no direct relationship to the map distance calculated based on crossover percentages |
| The distance measured in Map unit or centiMorgan | The distance measured in base pairs (bp, Kbp, Mbp) |
| Linear order is identical as in the physical map | Linear order is identical as in the genetic map |
| The relative distance between two genes | The exact location of genes in the chromosomes |