Adult mice were trained to execute a nose-poke in a port containing one of two simultaneously present odors in order to obtain a reward. Hippocampus RNA of trained mice vs. controls was subjected to Illumina deep sequencing. Two mitochondrial RNAs (a tRNA and Mt-1) gave rise to 25-30-nt. small RNAs that showed a dramatic and specific increase with training (>50-fold relative to controls). Mt-1 is encoded within the termination association sequence (TAS) of the mitochondrial DNA control region. Small RNAs may link behavioral plasticity to protein synthesis and replication of mitochondria to support dendritic growth, spine stabilization, and synapse formation.