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This study investigated the influence of whalewatching boats on the behaviour of gray whales on their migratory route in Todos Santos Bay, near the port of Ensenada, Baja California, Mexico. The objectives were: (1) to compare the swimming direction and velocity of whales in the presence and absence of whalewatching vessels, and when other boats were fishing, cruising or drifting; and (2) to contribute scientific data to the improvement of whalewatching regulations for Todos Santos Bay and surrounding waters. During the winters of 1998 and 1999, theodolite tracking was undertaken from a lighthouse tower located on northern Todos Santos Island. During both years, the migration corridor was about 2.5km wide at the Todos Santos Islands; this is relatively narrow compared to other shore stations along the northern coast (USA). Sightings were separated into northbound or southbound migration routes and the variability of whale swimming direction was analysed by circular statistics. During the southbound migration, whale swimming direction was not different in the presence or absence of whalewatching vessels and other boats. This variable, however, was statistically different during the northbound migration both with whalewatching vessels (p = 0.007) and with other boats (p = 0.02). Whale swimming velocity showed significant differences without boats and with whalewatching boats during both migrations (northbound, p = 0.04; southbound, p < 0.001). Analysis of velocity in the absence and presence of other boats did not yield significant differences for either of the migrations. In addition, a head-on approach by whalewatching boats changed the whales’ swimming direction (p = 0.05) and velocity (p = 0.015) significantly when compared with an approach towards the rear or flanks. Although Mexican whalewatching law is explicit concerning manoeuvres around whale groups, an additional suggestion is made here to prevent unintentional head-on approaches.