By comparing DNA sequences, the team revealed that two populations of tigrina in Brazil do not interbreed and are evolutionarily distinct.
Results also show the two populations have contrasting interactions with the closely related pampas cat and Geoffroy's cat.
There are at least seven species of small wild cat in the genus Leopardus in Central and South America, which are thought to have first colonised the region during the late Pliocene (2.5 - 3.5 million years ago).
A team of researchers led by Dr Eduardo Eizirik from the Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil collected samples of DNA from pampas cats (Leopardus colocolo) in the north of the country, Geoffroy's cats (L. geoffroyi) from the south and two separate populations - north eastern and southern - of tigrina (L. tigrinus).
"We used several different types of molecular markers to investigate the evolutionary history of these species," explained Dr Eizirik.
"These [molecular markers] evolve at different rates, which helps in the sense that they provide information on different time frames," he said.
By comparing these different chromosomal and mitochondrial DNA marker sequences the scientists could track patterns of interbreeding - or hybridisation - between the cat species and populations.
The markers revealed that the southern population of tigrina were actively breeding with Geoffroy's cat in areas where the two species came into contact. In contrast, they found evidence for ancient hybridisation between the north eastern tigrina and the pampas cat.
But what surprised Dr Eizirik and his colleagues most was the lack of evidence for recent mating between the north eastern and southern tigrinas.
"This observation implies that these tigrina populations are not interbreeding, which led us to recognise them as distinct species," Dr Eizirik told BBC Nature.
"This species-level distinction between the tigrina populations we really did not expect to find," he said.
The rules of zoological nomenclature mean the north eastern tigrinas (pictured) remain Leopardus tigrinus
It is the rarer north eastern populations that will keep the original scientific name of Leopardus tigrinus because they live geographically closer to the type locality and the more common southern form that will acquire the newly recognised scientific name of Leopardus guttulus.
"Recognising a distinct tigrina species in Brazil highlights the need for urgent assessment of its conservation status...and it may be found to be threatened," Dr Eizirik told BBC Nature.
"[These results] illustrate how much is still unknown about the natural world, even in groups that are supposed to be well-characterised, such as cats," he explained.
"In fact there are many basic aspects that we still don't know about wild cats, from their precise geographic distribution and their diets to even species-level delimitation, as in this case."