C-type lectins (CTLs) play an important role in innate immune defense. In this study, we identified and characterized two CTLs (Lec1 and Lec2) from the tubeworm Alaysia sp. collected from a hydrothermal vent in Pacmanus. Lec1 and Lec2 possess the typical CTL domain but share low sequence identities (10.8%–20.4%) with known CTLs. Recombinant (r) of Lec1 and Lec2 bound to various PAMPs and a wide arrange of bacteria from neritic and deep-sea environments in a Ca2+-independent manner, but only rLec1 caused agglutination of the bound bacteria. The activities of rLec1 and rLec2 were most stable and highest at 4 °C, the ambient temperature of the hydrothermal vent, and decreased at higher temperatures. Both lectins inhibited bacterial growth in a highly selective manner and agglutinated the erythrocytes of fish, rabbit, and chicken in a Ca2+-dependent manner. These results provided the first insights into the functional properties of CTLs in deep-sea Alaysia sp.