AFLP markers suggest low population genetic differentiation of the black rockfish Sebastes schlegelii

• AFLP was used to investigate the genetic structure of Sebastes schlegelii.
• S. schlegelii showed high Nei's gene diversity.
• No genetic divergence among populations was found.
• All the populations of S. schlegelii shared one gene pool.

AFLP markers were used to investigate the population genetic differentiation among populations of Sebastes schlegelii from China and Japan. A total of 405 bands were amplified for 180 individuals from 9 populations by 3 pairs of selective primers. S. schlegelii exhibited high Nei's gene diversity with an average value of 0.29 for all populations. No significant genealogical branches or clusters corresponding to sampling localities were detected by UPGMA tree. The results of AMOVA analysis and pairwise FST values showed no genetic divergence among different geographic populations. The result of STRUCTURE demonstrated all populations of S. schlegelii examined in the study shared one single gene pool.