Ship hull fouling is recognized as an important vector for the introduction of nonindigenous species (NIS), which has been studied globally but no empirical works exist in the Southeast Pacific. The present study examined fouling organisms on the hulls of three ships in one international Chilean port, and compared them with those on settling plates and natural substrates. Also, genetic analyses were perfomed on the most common NIS recorded in order to explore number and potential origin of the genetic linages found. The highest number of total taxa and NIS were found on ship hulls, with three species identified as NIS in ship samplings. Settling plates displayed the largest number of taxa, with a large abundance of the invasive tunicate Ciona robusta, which also showed high mitochondrial genetic diversity. This study showed that Chilean coasts are subjected to both NIS colonization and propagule pressure through ship hulls. Biosecurity measures should urgently be taken on ship hulls along these coasts.