But scientists have now been able to date their presence to at least one million years ago – some 120,000 years earlier than previously recognized.
The team reports the discovery of these humans’ tools in the journal Nature.
The group says the finds bring a new dimension to our understanding of the history of Flores.
Lead author Adam Brumm told BBC News that the location and circumstances of the tools’ preservation meant human occupation of the island could extend deep into the past.
The diminutive creature’s unearthing was a sensation because it indicated a separate human species was living alongside us just 18,000 years ago.
A dig site there, known as Mata Menge, had already revealed tools dated to 880,000 years ago. Now, just 500m away but much deeper in the sediments, an international team has identified even older artefacts.