A filling unit (1) comprises: a plate (12) for resting a container to be filled; a housing (2) facing the plate (12) to receive container's mouth; a dispenser (3) which opens onto the housing (2) to dispense liquid substance towards the container. The plate (12) is movable towards or, vice versa, away from the dispenser (3). The housing (2) comprises a bottom wall (24), fitted with a first annular gasket (21), and an annular body (6), movable relative to the bottom wall (24) and fitted with a second annular gasket (22). With a container (90) of a first type positioned on the plate (12), the plate (12) is moved towards the dispenser (3) to bring container's mouth (91) into contact with the first annular gasket (21). With a container (95) of a second type positioned on the plate (12), the annular body (6) is moved towards the plate (12) to bring the second annular gasket (22) into contact with container's mouth (96).