Activity of the Mutator transposons of Zea mays varies in different tissues and at different stages of development. In the soma, Mu elements excise at a high frequency late in tissue development. In germ cells, Mu elements rarely excise, but they amplify and insert at high levels around the time of meiosis. At all other times, Mu elements can duplicate and insert at a low frequency. To determine whether the patterns of Mutator activity correlate with tissue or cell-specific transcription of the regulatory transposon MuDR, we used in situ hybridization to localize the sense MuDR transcripts, mudrA and mudrB, in pistillate florets and embryos of four different maize Mutator stocks. We found mudrA and mudrB transcripts uniformly distributed in all tissues of immature, meristem-rich florets and in both somatic and germinal tissues of mature florets. In mature flowers, transcripts of both genes accumulate to high levels in the tapetal (endothelium) layer surrounding the embryo sac. We also found transcripts from the antisense strand of the mudrA gene in all cell types in the florets. In developing embryos, all MuDR transcripts were present in all tissues. Different Mutator stocks had characteristic accumulation patterns that were maintained throughout embryo development.