FOXL2 is a forkhead transcription factor involved in eyelid development and in the development and adult function of the ovary in mammals. In mouse, we have previously suggested the existence of two mRNA isoforms of Foxl2 that result from an alternative polyadenylation. In this study, we characterize in depth the structure and expression of these two variants. We also describe an antisense transcript that overlaps the whole Foxl2 transcription unit. This antisense transcript, called Foxl2OS (for opposite strand), yields several isoforms resulting from alternative splicing. No significant coding region was found in the Foxl2OS sequence. Foxl2OS displays a pattern of expression very similar to that of Foxl2 in the gonads during development and at the adult age. RNA FISH experiments show that both transcripts are expressed in the same cells at the same time. We suggest that Foxl2OS is a noncoding antisense RNA that may be involved in the regulation of Foxl2. All in all our results provide new insights about the organization of the murine Foxl2 locus. This might help us understand its regulation and function.