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Tandemly arranged paralogous genes  lbe  and  lbl  are members of the  Drosophila  NK homeobox family. We analyzed population samples of  Drosophila melanogaster  from Africa, Europe, North and South America, and single strains of  D. sechellia ,  D. simulans , and  D. yakuba  within two linked regions encompassing partial sequences of  lbe  and  lbl . The evolution of  lbe  and  lbl  is highly constrained due to their important regulatory functions. Despite this, a variety of forces have shaped the patterns of variation in  lb  genes: recombination, intragenic gene conversion and natural selection strongly influence background variation created by linkage disequilibrium and dimorphic haplotype structure. The two genes exhibited similar levels of nucleotide diversity and positive selection was detected in the noncoding regions of both genes. However, synonymous variability was significantly higher for  lbe : no nonsynonymous changes were observed in this gene. We argue that balancing selection impacts some synonymous sites of the  lbe  gene. Stability of mRNA secondary structure was significantly different between the  lbe  (but not  lbl ) haplotype groups and may represent a driving force of balancing selection in epistatically interacting synonymous sites. Balancing selection on synonymous sites may be the first, or one of a few such observations, in  Drosophila . In contrast, recurrent positive selection on  lbl  at the protein level influenced evolution at three codon sites. Transcription factor binding-site profiles were different for  lbe  and  lbl , suggesting that their developmental functions are not redundant. Combined with our previous results on nucleotide variation in esterase and other homeobox genes, these results suggest that interplay of balancing and directional selection may be a general feature of molecular evolution in  Drosophila  and other eukaryote genomes.

Complex Interplay of Evolutionary Forces in the ladybird Homeobox Genes of Drosophila melanogaster