The tospovirus Tomato spotted wilt virus is damaging to capsicum and tomato crops in WA, QLD and SA. Crops infected with these viruses often have reduced yield and decreased marketable fruit, and when infection is early in the growing season total crops losses can occur. In the Perth metropolitan area and southern WA, TSWV is often found infecting capsicum and tomato crops as well as lettuce and celery. In QLD, TSWV occurs in all coastal and sub-coastal vegetable production areas. The virus is a major cause of crop loss in greenhouse capsicum crops on the North Adelaide Plain. TSWV is transmitted by thrips (4 species in Australia) in a circulative and propagative manner, particularly the western flower thrips which is a very efficient vector. TSWV has a large host range, of more than 900 species of weeds, ornamentals and field crops. As such, an important part of managing this disease for the tomato and capsicum industry includes resistant varieties. In recent years it has become apparent that there are resistance breaking strains of TSWV present in Australia. This study collected 19 new isolates of both resistance and non-resistance breaking strains of TSWV from WA (10), QLD and SA (9) and subjected them to next generation sequencing on an Illumina HiSeq 2000. The genomes have been assembled and compared by phylogenetic analysis and a recombination study, the results of which will be presented here.