The decreased Cu,Zn SOD activity (less than 5%) in a "null" SODCA1 Drosophila melanogaster strain isolated in our laboratory is due to the insertion of a truncated P element into the transcribed region of the Cu,Zn SOD gene. Using a cDNA Cu,Zn SOD probe from a wild type D. melanogaster (F allele) we isolated an EcoRI Cu,Zn SOD clone from an EMBL3 genomic library of the SODCA1 strain, subcloned it, restriction-mapped and partially sequenced it. The 2.5 kb clone consists of a wild-type 1.84 kb EcoRI fragment containing the Cu,Zn SOD gene previously isolated in our laboratory, with an insertion of 0.68 kb derived (by an internal deletion) from an autonomous, 2.9 kb P element. The insertion starts 21 bp upstream from the coding sequence and causes an 8 bp target site duplication characteristic of P elements. A point mutation in the second exon results in a replacement of Asn by Lys at position 96, confirming that the mature protein encoded by the SOCCA1 is the same one encoded by the S allele, commonly found in natural populations. The diminished expression of SODCA1 allele is most possibly due to a reduction of the rate of transcription attributable to the insertion of the P element.