The introduction of non-indigenous species (NIS), also known as alien species, is a pressing issue throughout the world nowadays, mostly linked to globalization. Transitional environments are particularly exposed to this threat due to the importation of seafood for either aquaculture or sale. According to the most recent observations, the Mar Piccolo of Taranto hosts 36 NIS positively identified, divided in 13 invertebrates, 15 macroalgae, and 8 planktonic species. This basin ranks third among the Mediterranean hot spots for seaweed introduction, after the Thau Lagoon (southern France) and the Venice Lagoon. Continuous monitoring activities are carried out to early identify new introductions and follow the fate of those already introduced.