C-type lectins are a superfamily of Ca-dependent carbohydrate-recognition proteins that function as pattern recognition receptors (PRRs) in innate immune system. In this study, a new C-type lectin was identified from the swimming crab Portunus trituberculatus (PtCLec1). The full-length cDNA of PtCLec1 was 873 bp encoding 176 amino acids. The predicted PtCLec1 protein contained a signal peptide and a single carbohydrate-recognition domain with a special YPD motif. The PtCLec1 transcripts were mainly detected in hepatopancreas and its relative expression levels were significantly up-regulated after the challenges of Vibrio alginolyticus, Micrococcus luteus and Pichia pastoris. The recombinant PtCLec1 (rPtCLec1) could bind all the tested pathogen-associated molecular patterns (PAMPs), including lipopolysaccharides (LPS), peptidoglycan (PGN) and glucan (GLU), and microorganisms, including V. alginolyticus, V. parahaemolyticus, Pseudomonas aeruginosa, Staphylococcus aureus, M. luteus and P. pastoris. It also exhibited strong activity to agglutinate bacteria and yeast in a Ca-dependent manner, and such agglutinating activity could be inhibited by d-galactose and LPS. Moreover, rPtCLec1 revealed antimicrobial activity against the tested Gram-negative (V. alginolyticus, V. parahaemolyticus and P. aeruginosa) and Gram-positive bacteria (S. aureus and M. luteus), and promoted the clearance of V. alginolyticus in vivo and hemocyte phagocytosis in vitro. Knockdown of PtCLec1 could down-regulate the expression of phagocytosis-related genes, but enhance the expression levels of prophenoloxidase (proPO) system-related genes, mannose-binding lectin (MBL), antimicrobial peptides (AMPs), MyD88 and Relish. All these results indicate that PtCLec1 might act as a PRR in immune recognition and an opsonin in pathogen elimination.