Origin and evolution of new genes contribute a lot to genome diversity. New genes usually form chimeric gene structures through DNA-based exon shuffling and generate proteins with novel functions. We investigated polymorphism of 14 chimeric new genes in Drosophila melanogaster populations and found that eight have premature stop codons in some individuals while six are intact in the population, four of which are under negative selection, suggesting the two evolutionary fates of new chimeric genes after origination: accumulate premature stop codons and pseudolize, or acquire functions and get fixed by natural selection. Different from new genes originated through RNA-based duplication (retroposition) which are usually testis-specific or male-specific expressed, the expression patterns of these new genes through DNA-based exon shuffling are temporally and spatially diverse, implying that they may have the potential to evolve various biological functions despite that they may become pseudogenes or non-protein-coding RNA genes.