In Ireland, aphids are the most abundant and damaging insect pests. They cause damage through direct feeding, but primarily through the transmission of plant viruses. Yellow Dwarf Viruses (YDV) are transmitted by aphids commonly found in Ireland and are a major threat to the tillage sector, with potential yield losses of up to 80% in severe cases. Aphid monitoring programmes are a critical component of Integrated Pest Management and Irish aphids are actively monitored across the country through a suction trap network. This generates samples daily that require sorting by hand followed by identification using morphological features by trained taxonomists. However, this becomes unfeasible as insect numbers in traps increase and availability of taxonomic expertise decreases. This PhD thesis developed and evaluated molecular based methods as alternatives to morphological identification to take full advantage of the sampling efforts. DNA metabarcoding and metagenomics were both able to identify species; however relative species abundance (RSA) was more challenging, with RSA within species only feasible using DNA metagenomics. In addition to determining the species and relative abundance it is also important to track clonal lineages, identify mutations conferring resistance and determine the presence of YDVs. An assay, AphidMASH, was developed to support this type of surveillance on individual aphids and was successfully used to identify the first case of additional mutations (M918L and L932F) conferring potential insecticide resistance in the English grain aphid. Finally, a digital droplet PCR assay was also successfully developed to enable quantification of two species of Luteovirus in both the host plant and aphid vector. Overall, the work presented in this thesis will improve pest monitoring programs, increase fundamental knowledge on aphids and the yellow dwarf viruses they vector and highlights how best we can maximise the diminishing availability of expert taxonomists.