: Individuals from the same clonal population of Daphnia magna were grown and animals were harvested as juveniles, subadults and adults. The total RNAs from the three life stages were fractionated by size and the small RNA fractions were used to construct libraries that were deep sequenced on an Illumina sequencer. Three datasets (submitted here) contain clean reads with adaptors clipped off and removed non-clipped reads, adaptor-only reads N reads and reads <10 nucleotides. These three datasets have been used to study microRNAs in D. magna.