We have applied the techniques of RAPD (random amplified polymorphic DNA) and AFLP (amplified fragment length polymorphism) to the analysis of the relationships among Artemia species and strains. RAPD markers were successfully employed to detect diversity and genetic differentiation among four species of brine shrimp: A. franciscana, A. urmiana, A. sinica, and A. parthenogenetica. Seventy, ten-base synthetic oligonucleotides were used to amplify a total of 458 distinct fragments. DNA polymorphisms were found in all the species examined; The highest percentage of polymorphic bands found in A. parthenogenetica, was 28.8 per cent. There are significant differences between bisexual sibling species and parthenogenetic populations. A. parthenogenetica provided 94 specific molecular markers, while bisexual sibling species gave 27 specific molecular markers. A. sinica is a species distinct from the other Old World bisexual species. AFLP were used to analyze 15 Artemia species and strains for genetic diversity. They are extremely sensitive to even a small sequence variation and more polymorphism than RAPD. Using only 10 pairs of primer combinations, we detected 580 AFLP bands of which were polymerphic. The RAPD and AFLP techniques are powerful DNA fingerprinting methods for classification of Artemia species and strains.