Ficolins, a kind of lectin containing collagen-like and fibrinogen-related domains (FReDs, also known as FBG or FREP), are involved in the first line of host defense against pathogens. In this study, two ficolins, namely, MrFico1 and MrFico2, from the giant freshwater prawn Macrobrachium rosenbergii were identified. In contrast to other ficolins, these two ficolins have no collagen-like domain, but such ficolins contain a coiled region and a FReD domain. Phylogenetic analysis showed that MrFico1 and MrFico2, together with two ficolin-like proteins from Pacifastacus leniusculus, belonged to one group. Quantitative RT-PCR (qRT-PCR) showed that both MrFico1 and MrFico2 were expressed in hepatopancreas, stomach and intestine, with the highest expression in stomach for MrFico1, compared to the highest expression in hepatopancreas for MrFico2. qRT-PCR analysis also showed that MrFico1 was obviously upregulated upon Vibrio anguillarium challenge, while MrFico2 was upregulated after challenged by V. anguillarium or white spot syndrome virus. Bacterium-binding experiment showed that MrFico1 and MrFico2 could bind to different microbes, and sugar-binding assay revealed that these two ficolins could also bind to lipopolysaccharide and peptidoglycan, the glycoconjugates of bacteria surface. Moreover, these two ficolins could agglutinate bacteria in a calcium-dependent manner, and the results of bacteria clearance experiment showed that both ficolins could facilitate the clearance of injected bacteria in the prawn. Our results suggested that MrFico1 and MrFico2 may function as pattern-recognition receptors in the immune system of M. rosenbergii.