Operation Sophia (formerly EU NAVFOR Med) is an ongoing European Union military operation, established in 2015 to interdict refugee smuggling routes in the Mediterranean Sea.
Who commands this operation?
The operation has their own website and include their Chain of Command at the bottom of their About Us page. Operation Sophia's current commander is Italian Rear Admiral Enrico Credendino. According to his Wikipedia entry and the entry on Operation Sophia, he has been the commander since it was formed in May of 2015.
Strategic control of the operation apparently flows from the Council of the European Union's Political and Security Committee. From the second page of the published decision that created the operation:
(10) The Political and Security Committee (PSC) should exercise, under the responsibility of the Council and of the HR, political control over the Union crisis management operation, provide it with strategic direction and take the relevant decisions in accordance with the third paragraph of Article 38 of the Treaty on European Union (TEU).
"HR" above refers to High Representative of the Union for Foreign Affairs and Security Policy.