Aphids are important agricultural pests with about 250 species known to cause damage by feeding on plant phloem and transmitting plant viruses. Current management relies primarily on the application of chemical insecticides, which can be deleterious to the environment, and the use of aphid resistant cultivars hampered by the presence of resistant aphid biotypes. We aim to develop novel biotechnology based approaches to better manage pestiferous aphids. To this end, we (i) identified and characterized aphid viruses, and (ii) analyzed a class of small RNA, microRNAs specific to aphids. We used transcriptome and small RNA sequencing datasets to identify viruses that naturally infect populations of various aphid species. We identified and characterized a new isolate of Aphid lethal paralysis virus, named ALPV-Ap (Dicistroviridae) from the pea aphid, Acyrthosiphon pisum and a novel virus from the soybean aphid, Aphis glycines, named Aphis glycines virus (AGV; Unclassified). ALPV-Ap, which has a longer genome than other ALPV isolates, is phylogenetically closely related to ALPV isolates from honeybees rather than from aphids. ALPV-Ap localizes to the aphid midgut and is not vertically transmitted from adult to nymph. AGV has a capsid protein similar to those of plant viruses while the RNA-dependent RNA polymerase is more closely related to those of insect viruses. Remarkably, AGV is 100% vertically transmitted. Analysis of small RNA datasets from various aphid species showed the presence of over 100 microRNAs. In addition to detection of many evolutionarily conserved miRNAs, a subset of 12 aphid-specific miRNA was identified. The wealth of information obtained from sequencing datasets will allow for investigation of virus and miRNAs based management of aphid populations for reduced damage and increased crop yield worldwide.