He then held the position of director of the Antiquities Service in Tunisia between 1906 and 1920, where he was one of the pioneers of the exploration of the archaeological site of Dougga, between 1901 and 1902.

In 1907 he was alerted by Greek sponge fishermen cruising between Sousse and Sfax on the existence of a cluster of columns mixed with debris of all kinds lying forty meters deep.

Merlin then enlisted local maritime authorities and financial support to launch the first campaign of underwater archaeological excavation on the Mahdia shipwreck.

He thus brought to the surface some Athenian art objects dating back to the first century B.C., including the famous Hermes bronze Dionysus, signed by the sculptor Boethus.

[1] The vast majority of works by Alfred Merlin consists of communications made to the Comité des travaux historiques et scientifiques :