| Feature | Markers | |||
| Phenotypic | Biochemical | Molecular | Cytogenetic | |
| Description | Visual morphological indicators | Biochemical molecules, like proteins (e.g., isoenzymes), metabolites (e.g., carbohydrates) | DNA fragments of known locations on the chromosome | Chromosome structure —visible by microscopy |
| Examples | Colour, shape and size of flowers, seeds, or leaves | Isoenzyme gene loci | SNP, SSR or microsatellites, RAPD, AFLP | FISH, GISH |
| Genomic coverage | Low | Low | High | Average |
| Specialized equipment requirement | No | Yes | Yes | Yes |
| Cost-intensiveness | Low | Average | High | High |