This data were generated by small RNA sequencing of soybean leaves infected with Phakopsora pachyrhizi, the asian soybean rust pathogen. Two soybean genotypes, PI594760B and TMG06_0011 were used for inoculation. Rust isolate "Dayton 13" was used to assess compatible interaction on both genotypes. The samples were collected at 24h, 48h, and 72h post inoculation. Control samples was treated with mock inoculation and collected at 48h post inoculation.