Skrydlov became commander of the Russian Pacific Squadron from 1900-1902, and then of the Black Sea Fleet from 1903-1904. After the death of Admiral Stepan Makarov in combat during the Russo-Japanese War, Skrydlov was reappointed commander of the Russian Pacific Squadron on 1 April 1904. However, due to the Japanese blockade of Port Arthur, he was unable to reach his command, and returned from Vladivostok to St Petersburg on 20 December 1904 to accept an appointment to the Admiralty Board. He again commanded the Black Sea Fleet from 1906-1907, and retired from active service in August 1909 with the rank of admiral.