This collection is notable for its variety, with flags, full uniforms, insignia, items of clothing or fragments and ornaments, many of them from donations, while others come from naval combat.

The uniform collection contains outstanding pieces that belonged to illustrious sailors. These include the frock coat of Royal Navy Brigadier Casto Méndez Núñez from 1866, the pointed hat of Federico Gravina y Napoli, the two-cornered hat and sash of José María Beránger y Ruiz de Apodaca, the admiral's uniform of King Alfonso XIII's Kaiserlichen Deutschen Marine, and the gala uniform of His Majesty King Juan Carlos I, Captain General of the Spanish Navy.

The vexillia collection brings together pieces of great historical value, such as the flag of the "Príncipe de Asturias", which took part in the battle of Trafalgar, the flag of the sixth regiment of the Malaga line infantry of Joseph I Bonaparte's army, the flag of the French ship "Héros", fragments of the battle flag of the cruiser "Vizcaya", sunk in the naval battle of Santiago de Cuba in 1898, and the flag of the United States of America carried by the brig "Sawanah", captured by the Spanish 3rd-class cruiser "Elcano", among others.

Within this collection, the royal standard of the Oquendo family, from the last quarter of the 16th century, the confectioner of the Ducal House of Fernán Núñez, from the end of the 17th century, or the standard of the French Imperial Navy that belonged to the ship l'Atlas, considered the only standard of Napoleon I's Imperial Navy that has survived to the present day, are very remarkable and stand out for their singularity.

The Naval Museum also has an interesting collection of decorations from 19th to 20th centuries, mainly made up of specimens awarded to sailors as prizes for their military actions, although it also includes rewards awarded for services or merits in the civilian sphere. Thus, there are insignia and decorations of the Royal and Very Distinguished Order of Carlos III, the Royal and Naval Order of María Cristina, and the Royal and Military Order of San Hermenegildo.