As you are working on population genetics I agree on the use of microsatellite markers and/or mtDNA. With regard to the use of AFLPs, these are rarely used in animal population genetics when one aims to publish their data. Nevertheless, quit a few published articles in the last year measured the levels of genetic diversity and delineated population genetic structure in several elasmobranch species using AFLPs. Then again as said by our colleagues it depends on your research question.