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Due to its peculiar morphological characteristics, there is dispute as to whether the genus of <i>Annamocarya sinensis</i>, a species of Juglandaceae, is <i>Annamocarya</i> or <i>Carya</i>. Most morphologists believe it should be distinguished from the <i>Carya</i> genus while genomicists suggest that <i>A. sinensis</i> belongs to the <i>Carya</i> genus. To explore the taxonomic status of <i>A. sinensis</i> using chloroplast genes, we collected chloroplast genomes of 16 plant species and assembled chloroplast genomes of 10 unpublished <i>Carya</i> species. We analyzed all 26 species’ chloroplast genomes through two analytical approaches (concatenation and coalescence), using the entire and unique chloroplast coding sequence (CDS) and entire and protein sequences. Our results indicate that the analysis of the CDS and protein sequences or unique CDS and unique protein sequence of chloroplast genomes shows that <i>A. sinensis</i> indeed belongs to the <i>Carya</i> genus. In addition, our analysis shows that, compared to single chloroplast genes, the phylogeny trees constructed using numerous genes showed higher consistency. Moreover, the phylogenetic analysis calculated with the coalescence method and unique gene sequences was more robust than that done with the concatenation method, particularly for analyzing phylogenetically controversial species. Through the analysis, our results concluded that <i>A. sinensis</i> should be called <i>C. sinensis</i>.