During development of the sea urchin Strongylocentrotus purpuratus embryo, transcription of the Spec1 and actin CyIIIa genes is activated and the corresponding mRNAs accumulate specifically in ectoderm cells. We show that in gastrulae this tissue specificity of mRNA accumulation is regulated largely if not entirely at a posttranscriptional level. We used RNAase protection assays with intron and exon probes to measure the levels of nuclear precursors and mature message, respectively, in total RNA from embryo fractions enriched for ectoderm (Ect) or endoderm+mesenchyme (E/M) cells. These measurements demonstrate that E/M cells, which do not accumulate Spec1 and actin CyIIIa mRNAs, contain high levels of intron transcripts, indicating that cells of the E/M tissues transcribe these genes. At later stages, transcripts containing intron sequences are restricted to ectoderm cells. These results indicate that there is a transition from posttranscriptional to transcriptional regulation of tissue-specific mRNA accumulation during the gastrula stage. Measurements of transcription rate by nuclear run-on assays substantiate this conclusion for Spec1 and extend it to two other genes, SpEGFI and Spec2c, which also encode ectoderm-specific mRNAs. Posttranscriptional regulation was not observed for the SM50 gene whose mRNA accumulates only in primary mesenchyme cells, or for actin CyI which is expressed predominantly in E/M cells of gastrulae.