The Mediterranean Sea is considered a novel habitat that comprises extensive diversity of non-indigenous marine species. Here, we present an additional –but comprehensive– description of the newly recorded burrowing goby Trypauchen vagina on the southern coast of the Mediterranean Sea. In total, 53 individuals had been recorded as a bycatch collected using the beach seine netting method in 2021 on the Port Said coast. Morphometric and meristic characters were studied in 12 samples, and species identity was further confirmed by COI barcoding technique that revealed high similarity with T. vagina inhabiting the Indo-pacific region. Given that the current record represents the largest recorded bycatch size of T. vagina in the Mediterranean Sea, therefore, our study broadens the knowledge on the occurrence and abundance of that species off the southern coast. In this context, we highlighted the potential challenges encountered by the Mediterranean Sea environment facing the growing diversity of non-indigenous marine organisms.