A method of manufacturing mask alignment marks on an active surface of a semiconductor substrate (12) is disclosed, in which first, at least one layer (13) of a material resistant to oxidation is formed on the active surface, after which by a local etching of this layer, zones (15') for isolation by a field oxide, are defined simultaneously with the alignment marks (17'). There are formed, after the local etching of the layer (13) of anti-oxidation material while using the remaining parts of the anti-oxidation layer as a mask, depressions (26) at the substrate surface of a given depth at least at locations containing the alignment marks, which locations are designated as alignment windows (18) and the surface of the substrate is then exposed within the windows, and finally a thermal oxidation step is effected to obtain the field oxide (19'), during which the alignment marks (18) are simultaneously covered by oxide (24).