Can anyone tell me how botonisits determine whether flora or fawna is native to a given place?

What means do they use to determine if plants grew in a certain area thousands of years ago? I know that many settlers brought to Australia roses, geraniums, and lots of trees from their native countrires, because they were homesick and wanted a slice of home. But how do we know some of the flora and fawna didn't exist here prior to the introduction from people immigrating?