The university's project leader Michelle van der Bank said recording the deoxyribonucleic acid (DNA) of alien species was a step in tackling their invasion and spread.
"South Africa faces one of the largest problems with invasive plant species in the world, with the fynbos biome being a particular vulnerable vegetation type," she said.
"In the future, border checks may be provided with molecular tools to identify invasive plants and animals enabling prevention of prohibited species entering South Africa."
More than 660 alien plant species had established themselves in natural areas.
The most dramatic impact of invasive animal species was in rivers, where carp and bass had out-competed native fauna. About 60 percent of endemic freshwater fish were under threat.
Van der Bank said 13 snail species had established invasive populations and 40 of the 42 major invertebrate crop pests were not native to the country.
"This raises serious concerns about the future of our agriculture and ecosystem-related services."
A team of botanists and zoologists would visit different reserves between Sunday and April 27, to collect DNA of both native and alien species.
The project forms parts of the International Barcode of Life project, which aims to assemble a barcode reference library for all life on Earth.
The international project had identified 66,000 species and was aiming for a further 50,000 species by 2015.
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