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In this paper we propose and study a hybrid discrete–continuous mathematical model of collective motion under alignment and chemotaxis effect. Starting from paper [23], in which the Cucker-Smale model [22] was coupled with other cell mechanisms, to describe the cell migration and self-organization in the zebrafish lateral line primordium, we introduce a simplified model in which the coupling between an alignment and chemotaxis mechanism acts on a system of interacting particles. In particular we rely on a hybrid description in which the agents are discrete entities, while the chemoattractant is considered as a continuous signal. The proposed model is then studied both from an analytical and a numerical point of view. From the analytic point of view we prove, globally in time, existence and uniqueness of the solution. Then, the asymptotic behaviour of a linearised version of the system is investigated. Through a suitable Lyapunov functional we show that for t → +∞, the migrating aggregate exponentially converges to a state in which all the particles have a same position with zero velocity. Finally, we present a comparison between the analytical findings and some numerical results, concerning the behaviour of the full nonlinear system.