On the trip during which Anubis grounded on San Miguel Island,a passage from Tacoma, Washington, to Hamburg, the vessel had already experienced misfortune; in San Francisco, three crewmen were detained by United States authorities for assault on Chief Officer Johannes Dohrn and while departing San Francisco, Anubis missed colliding with the steamer Cecil by a mere 10 feet (San Pedro Daily Pilot, 21 Jul and 30 Jul 1908). More was to come.

This vessel stranded near San Miguel Island, off course due to a faulty compass and fog on 20 July 1908. Some early newspaper accounts and one of the two wreck reports for this vessel located the wreck site "on a reef of death between Santa Rosa and San Miguel Islands" (San Pedro Daily News, 21 Jul 1908), but the stranding actually occurred between Castle Rock (Flea Island) and San Miguel Island. Anubis grounded less than two miles away from the lumber schooner J M Colman, wrecked only three years earlier. "The Anubis struck the rock at 12:15 o'clock Monday morning, while running at eight knots through a heavy fog. For a mile before the disaster the keel moved through a bed of kelp. Captain Von Salzen was asleep at the time. He had left word that he should be called if fog was encountered, but this order was disobeyed.

By July 25, the steamer San Diego had returned to San Pedro with 600 sacks of flour from Anubis (Los Angeles Herald, 26 Jul 1908). Other vessels, including one under the command of Captain Ira Eaton, removed about 1800 tons of cargo by the end of the month. Apparently swelling sacked barley in the lower hold sealed some of the holes opened up in the grounding. Anubis was pulled off the rocks, repaired temporarily in Cuyler Harbor, and returned to San Francisco by the tug Goliath by August 17. Morris & Lima