AbstractWe have analyzed nucleotide polymorphism within a 5.3-kb region encompassing the functional Est-6 gene and the ψEst-6 putative pseudogene in 28 strains of Drosophila melanogaster and one of D. simulans. Two divergent sequence types were detected, which are not perfectly associated with Est-6 allozyme variation. The level of variation (π) is very close in the 5′-flanking region (0.0059) and Est-6 gene (0.0057), but significantly higher in the intergenic region (0.0141) and putative pseudogene (0.0122). The variation in the 3′-flanking region is intermediate (0.0083). These observations may reflect different levels of purifying selection in the different regions. Strong linkage disequilibrium occurs within the region studied, with the largest values revealed in the putative pseudogene and 3′-flanking region. Moreover, recombination is restricted within ψEst-6. Gene conversion is detected both within and (to a lesser extent) between Est-6 and ψEst-6. The data indicate that ψEst-6 exhibits some characteristics that are typical of nonfunctional genes, while other characteristics are typically attributed to functional genes; the same situation has been observed in other pseudogenes (including Drosophila). The results of structural entropy analysis demonstrate higher structural ordering in Est-6 than in ψEst-6, in accordance with expectations if ψEst-6 is indeed a pseudogene. Taking into account that the function of ψEst-6 is not known (but could exist) and following the terminology of J. Brosius and S. J. Gould, we suggest that the term “potogene” may be appropriate for ψEst-6, indicating that it is a potential gene that may have acquired some distinctive but unknown function.