The heat-inducible genes encoding 16-kD heat shock polypeptides in Caenorhabditis elegans are found at two separate loci, one containing the 16-1 and 16-48 genes (locus A), and the other, the 16-2 and 16-41 genes (locus B). Despite the highly conserved structures of these genes and their promoters, the B locus produces up to sevenfold more mRNA during heat induction than does the A locus. Since there are two copies of the 16-1 and 16-48 genes at the A locus, the discrepancy in mRNA production is actually as high as 14:1 on a per gene basis. Measurements of the rate of hsp16 mRNA decay during recovery from a heat shock suggest that this difference is not caused by differential mRNA stability; furthermore, nuclear runon experiments yield rates of transcription for the 16-1/48 locus that are approximately threefold higher than those from the 16-2/41 locus. The higher levels of mRNA from the 16-2/41 locus, particularly at longer induction times, seem to be due to a marked difference in the temporal pattern of mRNA production from the two loci. While both loci are transiently activated by a heat shock, the 16-1 and 16-48 genes of the A locus are down-regulated to a lower transcription rate sooner than the genes from the B locus.