Australia's only species of the endangered fishing bat, or micro-bat, have been recorded breeding and roosting in Sydney, surprising researchers.

The Large-footed Myotis, normally associated with freshwater, for the first time has been found living around Sydney Harbor, Fairfax media reported on Thursday.

Authorities found the bats in January 2014 as part of a local survey of bat populations.

A new study has shown the endangered bat lives across the Sydney region, though most activity is concentrated in hot spots.

NSW Department of Primary Industries biodiversity researcher Dr Leroy Gonsalves said the findings, along with a number of other endangered bat species previously unrecorded, proves that ecologists need to get out and look for species.

"If ecologists aren't out there, how will we know [the bats] are there and how can we manage and how can we protect them?" Gonsalves told Fairfax Media.

The micro-bats use their long clawed feet to scrape the water for fish and insects