Using an unbiased deep sequencing approach, we sequenced and assembled the genomes of six viruses that we found in soybean aphids (Aphis glycines) obtained from Michigan, Ohio, Iowa and China. Our study is the first research survey on virus sequences in the soybean aphid, and the first to identify any viruses in the soybean aphid. The large samples allowed us to be more informed on the viruses the soybean aphids carried, and the deep sequencing allowed us to study multiple viral populations in the most cost- and time-efficient way. The results reveal known and novel viruses, which provide valuable information on viral diversity and evolution.