Physical mapping is an alternative approach to genetic mapping in which specific locations on the genome are identified using DNA based map features. Unlike genetic mapping that uses recombination frequency to measure distances, physical mapping relies on actual physical characteristics of the DNA sequence.

The units or map features used in physical mapping include restriction enzyme sites (restriction mapping), Simple Sequence Length Polymorphism (SSLP), and Sequence Tagged Sites (STS). These features serve as landmarks that help identify specific positions on the genome.

Restriction mapping involves the use of restriction enzymes that cut DNA at specific base sequences. This results in DNA fragments that can be visualised by agarose gel electrophoresis, where DNA fragments are separated based on their sizes. The pattern of restriction sites provides a physical map of the genome.

SSLP and STS are other important map features used in physical mapping. These features are helpful in creating a high resolution physical map of the genome, allowing for more precise identification of gene locations compared to genetic maps which are sparsely populated due to limited availability of genetic loci.

Physical mapping overcomes the main drawback of genetic mapping, which is the limited number of genetic loci responsible for known phenotypes. This makes physical maps more useful for fine mapping of new phenotypes to the genome.