This paper presents morphometric and genetic barcoding analyses of the first record of the Cocoa Damselfish, Stegastes variabilis in the Mediterranean Sea. A single specimen was captured from Senglea waterfront, Malta (Central Mediterranean) on the 15th of September 2013. The species is non-indigenous in the Mediterranean, as it is native to the tropical Western Atlantic. Apart from undertaking identification through meristics and morphometric measurements of the specimen, genetic analyss of the 3410 bp mtDNA genes were carried out to confirm the species' identity. The latter was useful given that the genus Stegastes is known to be composed of morphologically very similar species, with variable colour patterns.