| Feature | ISSR | RAPD | SCAR |
| Plant material required | Little | Little | Little |
| Information generated | High and specific | High and nonspecific | Low and specific |
| Time required for detection | Short | Short | Short |
| Loci (single/multiple) | Multiple/single | Multiple | Single |
| Principle | DNA amplification | DNA amplification | DNA amplification |
| PCR based markers | Yes | Yes | Yes |
| Reproducibility | Moderate | Moderate | High |
| Part of genome | Whole genome | Whole genome | Part of genome |
| Use and development | Difficult | Moderate | Low |
| Reliability | High | Low | High |
| Use of radioactivity | No | Yes/No | No |
| Development time | Long | Short | Short |