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Abstract Diatoms, a major group of microalgae, play a critical role in global carbon cycling and primary production. Despite their ecological significance, comprehensive genomic resources for diatoms are limited. To address this, we have annotated previously unannotated genome assemblies of 49 diatom species. Genome assemblies were obtained from NCBI Datasets and processed for repeat elements using RepeatModeler2 and RepeatMasker. For gene prediction, BRAKER2 was employed in the absence of transcriptomic data, while BRAKER3 was utilised when transcriptome short read data were available from the Sequence Read Archive. The quality of genome assemblies and predicted protein sets was evaluated using BUSCO, ensuring high-quality genomic resources. Functional annotation was performed using EnTAP, providing insights into the biological roles of the predicted proteins. Our study enhances the genomic toolkit available for diatoms, facilitating future research in diatom biology, ecology, and evolution.