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As an endosymbiont, <i>Wolbachia</i> exerts significant effects on the host, including on reproduction, immunity, and metabolism. However, the study of <i>Wolbachia</i> in Thysanopteran insects, such as flower thrips <i>Frankliniella intonsa</i>, remains limited. Here, we assembled a gap-free looped genome assembly of <i>Wolbachia</i> strain <i>w</i>FI in a length of 1,463,884 bp (GC content 33.80%), using Nanopore long reads and Illumina short reads. The annotation of <i>w</i>FI identified a total of 1838 protein-coding genes (including 85 pseudogenes), 3 ribosomal RNAs (rRNAs), 35 transfer RNAs (tRNAs), and 1 transfer-messenger RNA (tmRNA). Beyond this basic description, we identified mobile genetic elements, such as prophage and insertion sequences (ISs), which make up 17% of the entire <i>w</i>FI genome, as well as genes involved in riboflavin and biotin synthesis and metabolism. This research lays the foundation for understanding the nutritional mutualism between <i>Wolbachia</i> and flower thrips. It also serves as a valuable resource for future studies delving into the intricate interactions between <i>Wolbachia</i> and its host.