The present study reports polychaetes that bore into limestone rocks along the east coast of the Aegean Sea (eastern Mediterranean). Rock materials were collected at two depth intervals (0–5 and 5–10 m) at 15 stations in four localities of Ildırı Bay. A total of 276 specimens belonging to 12 species and four families (Eunicidae, Spionidae, Cirratulidae and Sabellidae) were recorded. Specimens belonging to Dodecaceria and Pseudopotamilla were identified at the genus level, because they differ from described species, were few in number or were in poor condition. Dipolydora giardia is a new species to the marine fauna of Turkey. The most dominant and frequent family in the area was Eunicidae, followed by Spionidae. Lysidice ninetta and L. margaritacea comprised 59% of the total number of individuals. The number of species and individuals, and the diversity index did not change with regard to depth or locality. Two species assemblages were found in the area, mainly formed by Dipolydora and Lysidice species. The Lessepsian species, Palola valida, which is a new record for the Aegean Sea, occurred abundantly at the study sites, posing a risk of damage to limestone rocks in the Mediterranean Sea. The morphological features of the species identified at the generic level and the burrow structure of these species are presented. The burrow shapes of Palola siciliensis and P. valida were described for the first time in the present study; they constructed complicated galleries, including more than four entrances.