This study deals with the structure of echinoderm assemblages and their relationships with the biotic and abiotic conditions in the Canakkale Strait in 2006 and 2007. A total of 25 echinoderm species were found, 4 species of which [Amphiura securigera (Duben & Koren, 1846); Amphiura lacazei Guille, 1976; Amphiura cherbonnieri Guille, 1972; and Thyone fusus (O.F. Muller, 1776)] were new records for Turkish fauna; 1 species [Ophiopsila annulosa (M. Sars, 1859)] was new for the Turkish Strait System; and 22 species were first reports for the Canakkale Strait. Echinocyamus pusillus (0.F. Muller, 1776), Amphipholis squamata (Delle Chiaje, 1829), and Ophiothrix fragilis (Abildgaard, 1789) were the most important species, representing 71% of the total abundance. Ophiuroids were found to be the dominant group, but asteroids also played a significant role in the echinoderm community structure. No seasonal differences were found, while finer sediments and the percentage of organic carbon (TOC) seemed to encourage echinoderm behavior. Hydrodynamism seems to be the factor regulating benthic assemblages' structure and distribution in the Canakkale Strait. An identification key to the Mediterranean species of the genus Amphiura is provided.