| Marker Name | PCR-based | Polymorphism (abundance) | Dominance | Reproducibility | Automation | Running cost |
| RFLP | No | Low/medium | Codominant | High | Low | High |
| RAPD | Yes | Medium/high | Dominant | Low | Medium | Low |
| SCARS/CAPS | Yes | High | Codominant | High | Medium | Medium |
| AFLP | Yes | High | Dominant | High | Medium/high | Medium |
| SSR | Yes | High | Codominant | High | Medium/high | Low |
| ISSR | Yes | High | Dominant | High | Medium/high | Low |
| STS | Yes | High | Codominant/ dominant | High | Medium/high | Low |
| SRAP/EST | Yes | Medium | Codominant | High | Medium | Low |
| IRAP/REMAP | Yes | High | Codominant | High | Medium/high | Low |
| SNP | Yes | Extremely high | Codominant/ dominant | High | High | Low |