Pig blastocysts exhibit a transient period of estrogen production at periimplantation, with a second, more sustained period of estrogen synthesis occurring in endometrium and placenta at later pregnancy. Previously we reported the isolation of cDNA clones encoding a novel isoform of cytochrome P450 aromatase (the terminal enzyme in the estrogen biosynthetic pathway) from porcine periimplantation blastocysts. The present study investigated pregnancy-associated expression, in blastocysts and maternal reproductive tract tissues of this and an additional mRNA transcript encoding a distinct P450 aromatase isoform. Restriction endonuclease and nucleotide sequence analyses of 44 cDNA clones demonstrated that the major aromatase mRNA in periimplantation blastocysts and early-pregnancy endometrium and placenta (blastocyst-type) differed in sequence from the major aromatase mRNA expressed in endometrium and placenta at midpregnancy (endometrial-type). The deduced blastocyst and endometrial aromatase isoform protein sequences had 93% similarity. A third type of aromatase mRNA, deleted in exons 4-6 sequences, also was cloned from blastocysts. This cDNA was identical in nucleotide sequence to the blastocyst full-length aromatase cDNA and specified an open reading frame of 354 amino acids for a putative aromatase-related protein containing the heme-binding domain. Expression of this shorter mRNA in blastocysts was confirmed by reverse transcription polymerase chain reaction. The 5'-untranslated exon sequences in the transcripts encoding the blastocyst-type aromatase isoform were distinct from that of the endometrial type, consistent with differential expression of multiple chromosomal genes. In periimplantation equine embryos, however, embryonic and placental 5'-untranslated exon-containing transcripts were coexpressed. Results identify an aromatase isoform expressed in the endometrium and placenta at midpregnancy, demonstrate a transition in synthesis of aromatase isoform-specific mRNAs during placental development, and suggest the preferential involvement of the blastocyst aromatase isoform in synthesis of estrogenic molecules that may function in embryo-maternal signaling at periimplantation.