Macrophages are present in every tissue of the body. Acting as sentinels of the immune system, they have the ability to engulf apoptotic cells and pathogens and also produce effector signals to mount a proper immune response. In response to tissue injury or microbe invasion, they are rapidly recruited to the injured site and are main key players in the protection of the host. Associated with many diseases, macrophages can have deleterious roles, especially due to their pro-inflammatory function. However, macrophages were discovered to be central during the orchestration of every step of inflammation, from initiation to resolution phases and to participate in tissue development, homeostasis and repair. These plural functions exerted by macrophages support their high plasticity and versatility potential and suggest the existence of macrophage subsets that might be differentially activated and/or recruited during physiological and pathological processes. The study of macrophage behaviour dynamics and functions in their activated states requires tractable in vivo models in which macrophages can be visualized under physiological or stress conditions. Thus, the zebrafish (Danio rerio) has emerged as an excellent vertebrate system to study myeloid development, inflammation and host-pathogen interactions. Conservation of immune cell lineage, optical accessibility of the zebrafish embryo combined with genetic approaches unable us to improve our understanding of macrophage functions. In this review, we discuss recent studies that have used the zebrafish advantages to provide key advances in the field of vertebrate macrophage biology and functions. To cite this article: Nguyen-Chi Mai, et al. Deciphering the complexity of macrophage biology and function with the zebrafish model. Macrophage 2016; 3: e1260.