Alexander Justham will take up the position following Sally Dewar's internal move to become managing director of wholesale and institutional markets.
Justham will take on responsibility for the UK Listing Authority (UKLA), market monitoring, the supervision of exchanges and the oversight of the clearing and settlement infrastructure.
He has been with the FSA for just over a year following his move from JP Morgan in January 2007.
Dewar said of her successor: "I am delighted Alexander will be taking on the role of director of markets. He brings a wealth of valuable experience to the FSA and he is highly regarded.
"I have enjoyed working with him since he joined us last year and look forward to working closely with him in his new role."
