Fall armyworm (Spodoptera frugiperda) is a noctuid moth from the Americas with a broad host range that threatens a range of important crops. It consists of two morphologically indistinguishable strains (‘corn’ and ‘rice’) that have different host plant preferences. It was detected for the first time in Australia in 2020 following its rapid dispersal through Africa and Asia. Species identification of S. frugiperda in 48 specimens from seven locations in the Northern Territory was confirmed by DNA barcoding and morphological assessment. The majority of specimens possessed the mitochondrial haplotype associated with the ‘rice-strain’, whereas two specimens had a haplotype identified as the ‘corn-strain’. The two mitochondrial haplotypes observed in our study are identical to the most common haplotypes previously observed in Africa. Analysis of a nuclear gene identified all specimens as ‘corn-strain’. The agreement of both mitochondrial and nuclear markers as ‘corn-strain’ haplotypes occurred in two samples only, suggesting discrepancies between the mitochondrial and nuclear markers analysed. As fall armyworm spreads to other locations in Australia, further monitoring and genetic characterization of populations is recommended to investigate strain, genetic diversity and population structure. Monitoring of populations in association with host plant preferences will provide valuable information on host plant preferences and strain characterisation.