In this study, we obtain and analyze the first transcriptome data for the family Thamnocephalidae, targeting Branchinella kugenumaensis (Ishikawa, 1895), an anostracan fairy shrimp primarily found in Japan and Far Eastern Eurasia. We collected a male specimen from a rice paddy in Tochigi, Japan, and performed RNA-seq analysis, obtaining an assembled transcriptome comprising a 15,157 nucleotide sequence with an 80.75% completeness score. Because the relationships among the families within Anostraca remain unclear, using both mitochondrial and nuclear genes, we constructed phylogenetic trees employing maximum likelihood and Bayesian methods. Our results indicate that Artemiidae formed a cluster with Thamnocephalidae, and together they formed a sister group to the other Anostraca. We also demonstrated that a large number of parallel or back substitutions can hinder the estimation of phylogenetic relationships. This study not only enhances our understanding of anostracan phylogeny but also highlights the significance of transcriptome data in evolutionary biology.