We investigated soybean seed protein gene transcription during development. We found that seed protein genes are transcriptionally activated and then repressed during embryogenesis and that these genes are either inactive or transcribed at low levels in the mature plant. We further observed that genes encoding mRNAs with vastly different prevalences are transcribed at similar rates. DNA gel blot studies showed that transcriptionally active and inactive seed protein genes have indistinguishable methylation patterns. We conclude that both transcriptional and posttranscriptional processes regulate seed protein mRNA levels in the absence of detectable DNA methylation changes.