Balaustium medicagoense Meyer & Ryke (Acari: Erythraeidae) and Bryobia spp. Koch (Acari: Tetranychidae) are significant emerging pests in Australian grains and pastures. Despite this, there is limited information known on their basic biology, such as species status and reproductive modes, making it difficult to develop effective and sustainable control strategies. The species/strain status of Balaustium and Bryobia mites from southern Australia was examined using a combination of mitochondrial and nuclear DNA sequence data. In addition, the amplified fragment length polymorphism (AFLP) method was used to examine the reproductive mode and genetic diversity of Ba. medicagoense from 16 populations within southern Australia. Results indicate that there is only one species of Balaustium (Ba. medicagoense) and as many as seven species of Bryobia mites currently present in grain crops, pastures and roadsides within southern Australia. The Bryobia species complex consists of four recently described lineages (Bryobia sp. I, Bryobia sp. IV, Bryobia sp. VII, and Bryobia praetiosa Koch) and three additional genetic lineages (Bryobia sp. VIII, Bryobia sp. IX, and Bryobia sp. X) that have not been described previously. Bryobia sp. VIII, B. sp. IX, and B. sp. I seem to be the most abundant species present in Australian broadacre agriculture (i.e., land suitable for farms practicing large-scale crop [agriculture] operations). The AFLP data revealed that Ba. medicagoense reproduces asexually and that genetic diversity was low with only 10 genotypes found. These findings indicate a new complex of pest mites are present within Australian grain crops and pastures and this has implications for their control.