GeSeq is a web application designed for the rapid and accurate annotation of organelle genomes, particularly chloroplast genomes. It combines batch processing with a fully customizable reference sequence selection, including manually curated reference sequences from NCBI and user-uploaded references. GeSeq uses BLAT-based homology searches and profile Hidden Markov Models (HMMs) for protein and rRNA coding genes, as well as de novo predictors for tRNA genes. The application outputs a GenBank file that requires minimal curation and can be visualized using OGDRAW. Additional outputs, such as multi-FASTA files and codon-based alignments, facilitate downstream analyses. GeSeq is highly flexible, allowing users to select or upload custom reference sequences, making it suitable for various annotation tasks, including quick annotations, high-quality annotations of complete genomes, and the annotation of NGS-derived contigs. The tool aims to achieve high annotation quality while maintaining flexibility and ease of use.GeSeq is a web application designed for the rapid and accurate annotation of organelle genomes, particularly chloroplast genomes. It combines batch processing with a fully customizable reference sequence selection, including manually curated reference sequences from NCBI and user-uploaded references. GeSeq uses BLAT-based homology searches and profile Hidden Markov Models (HMMs) for protein and rRNA coding genes, as well as de novo predictors for tRNA genes. The application outputs a GenBank file that requires minimal curation and can be visualized using OGDRAW. Additional outputs, such as multi-FASTA files and codon-based alignments, facilitate downstream analyses. GeSeq is highly flexible, allowing users to select or upload custom reference sequences, making it suitable for various annotation tasks, including quick annotations, high-quality annotations of complete genomes, and the annotation of NGS-derived contigs. The tool aims to achieve high annotation quality while maintaining flexibility and ease of use.