For the first time since Russia annexed the territory in March, the city of Sevastopol hosted the ceremony - complete with warships parading through the bay and gunfire for spectators.
Thousands of people attended the celebration and many welcomed the turn of events.
Rear Admiral Yevgeny Khalaychev said: "This is a festival for all of Sevastopol's residents. This is a festival for Crimea's residents. This is a festival for all the Russian people. Because today, for the first time in many years, Sevastopol feels like a truly Russian city, a city of the Russian navy."
Due to the annexation, Ukraine moved its Navy Day ceremonies from Sevastopol across the Black Sea to Odessa.
At the port city's centre, Ukrainian navy officers paid tribute at the tomb of the unknown sailor.
Odessa is now home to most of the Ukrainian fleet.
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