Was Australia always known as Australia?

Not always.

The Australian continent was variously known as Locac or Lucach, India meridional (South India), Java le Grande and Terra Australis by Mercator (and others) during the late 1500s.

The name Australia is derived from the Latin phrase terra australis incognita meaning 'unknown south land' in reference to the as yet unknown land mass believed to lie in the south throughout the Middle Ages.

Portuguese sailor Pedro Fernández de Quirós (in portuguese Fernandes de Queirós), searched for this new land in 1606 while serving in the spanish navy, and called it Austrialia del Espíritu Santo or 'Great South Land of the Holy Spirit'. The word "Austrialia", slightly different from the current "Australia", was a mixture formed by "Austria" (the country of origin of the Habsburg dinasty) and "Austral" ("Southern"). In those times the current nations of Spain and Portugal were under the rule of the same crown. The word Austrialia was intended to be an homage to the ruling monarchs. Different variations on the name were used in many languages. There was, however, a German document dating back to 1545 describing a southern land mass as Australia.

Following Dutch exploration along the western coastline, the Dutch named the western half of the continent New Holland, whilst James Cook named the eastern half of the continent New South Wales, over 150 years after the Dutch.

After Matthew Flinders circumnavigated Australia, he then proposed the name Terra Australis, which became Australia, the name adopted in 1824.