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Background Gene prediction is an essential step in the annotation of metagenomic sequencing reads. Since most metagenomic reads cannot be assembled into long contigs, specialized statistical gene prediction tools have been developed for short and anonymous DNA fragments, e.g. MetaGeneAnnotator and Orphelia. While conventional gene prediction methods have been subject to a benchmark study on real sequencing reads with typical errors, such a comparison has not been conducted for specialized tools, yet. Their gene prediction accuracy was mostly measured on error free DNA fragments. Results In this study, Sanger and pyrosequencing reads were simulated on the basis of models that take all types of sequencing errors into account. All metagenomic gene prediction tools showed decreasing accuracy with increasing sequencing error rates. Performance results on an established metagenomic benchmark dataset are also reported. In addition, we demonstrate that ESTScan, a tool for sequencing error compensation in eukaryotic expressed sequence tags, outperforms some metagenomic gene prediction tools on reads with high error rates although it was not designed for the task at hand. Conclusion This study fills an important gap in metagenomic gene prediction research. Specialized methods are evaluated and compared with respect to sequencing error robustness. Results indicate that the integration of error-compensating methods into metagenomic gene prediction tools would be beneficial to improve metagenome annotation quality.