Lucina pectinata is a bivalve mollusk that lives in the Southwestern coast of Puerto Rico and houses intracellular symbiotic bacteria. This peculiar organism contains three types of hemoglobin, each characterized by distinct physico-chemical properties. Hemoglobin I (HbI) is a sulfide-reactive protein that reacts with H(2)S to form ferric hemoglobin sulfide. In contrast, hemoglobin II and III are oxygen-reactive proteins that remain oxygenated in the presence of hydrogen sulfide. The partial coding region contained in the cDNA sequences we have cloned confirmed the L. pectinata HbIII amino sequence reported in the NCBI protein database) with a single amino acid difference (Asn72Asp; AsnE12Asp). The characterization of the full length mRNA coding for L. pectinata HbIII revealed an alternative polyadenylation site and an alternate transcription start site. The open reading frame (ORF) of the HbIII cDNA is composed of 459nts containing 153 codons. The initiation codon is preceded by 62 nts of untranslated region (5'UTR), whereas two 3'UTR regions of 640 nt and 455 nt long were identified, revealing the presence of alternative polyadenylation sites. Isoforms of the 3'UTR of HbIII only differed in the length of their sequences. It has been hypothesized that alternative polyadenylation acts through shortening of mRNA to regulate RNA localization, translation and stability. Interestingly, the HbIII mRNA is the only one of all the hemoglobin mRNAs from L. pectinata characterized so far with more than one 3'UTR. Primer extension products suggest two closely located start sites of HbIII mRNA transcription. We suggest that the L. pectinata hemoglobin genes may be under different cellular controls that direct them to exert their particular functions. These hypotheses need to be tested by functional studies and analysis of the regulatory elements of the cognate genes for L. pectinata hemoglobins.