The streptococcal M protein family, a number of cell surface molecules that interact with the human immune system, can be divided into two major classes, A and C, characterized by different types of repeats in the central part of the molecule. Class A and class C molecules are known to have a variable N-terminal region and a more conserved C-terminal region, but little is known about the mechanisms that give rise to this structural variation. In this report, we show that two variants of protein Arp, an IgA receptor in class C of the M protein family, have virtually identical signal sequences and C-terminal halves, but unrelated N-terminal sequences. Comparison of the sequences of the two genes and their flanking regions also demonstrates the presence of well-defined variable and conserved regions. Our results strongly suggest that the N-terminal sequence variation between the two variants of protein Arp was generated through an intergenic recombination event, rather than through intragenic recombination or accumulation of mutations.