As a plant-specific transcription factor, the NAC (NAM, ATAF1/2 and CUC2) domain protein plays an important role in plant growth and development, as well as stress resistance. Based on the genomic data of the cacao tree, this study identified 102 cacao NAC genes and named them according to their location within the genome. The phylogeny of the protein sequence of the cacao tree NAC family was analyzed using various bioinformatic methods, and then divided into 12 subfamilies. Then, the amino-acid composition, physicochemical properties, genomic location, gene structure, conserved domains, and promoter cis-acting elements were analyzed. This study provides information on the evolution of the TcNAC gene and its possible functions, laying the foundation for further research on the NAC family. Genes 2020, 11, 35 2 of 11 hormone signaling [23,24]. In total, 166 species with NAC genes were identified. For example, there are 105 in Arabidopsis [25], 151 in Oryza sativa [26], 142 in Vitis vinifera [27], 163 in Populus trichocarpa [28], 113 in Prunus mume [29], 63 in Coffea canephora [30], and 152 in the soybean genome [31]. However, NAC genes were not studied in Theobroma cacao.Theobroma cacao, also known as the cacao tree, belongs to the Malvaceae family and is one of the world s three major beverage crops. Cocoa beans are the seeds of cacao trees and are the main raw material for chocolate. Globally, 3.7 million tons of cocoa beans are produced per year; however, diseases and pests cause harvest losses of about 30%. Determining the genes associated with cacao tree resistance is a key issue in its genetic breeding. Cacao trees also have high economic value because the cacao flavanols provide health benefits, which can be used in nutritional products [32][33][34], and cocoa polyphenols such as catechin and epicatechin have significant antioxidant properties and free radical-scavenging ability. To date, most studies of cacao trees focused on their active components; there were few studies at the genome level. The genome of the cacao tree was completed and published in 2011 [35], providing a powerful tool for studying the cacao tree at the gene level.Many studies showed that, after plant stress, the NAC transcription factor family is involved in the regulation of responses to environmental stress [36]. Overexpression of TsNAC1 in Thellungiella salsuginea can increase abiotic stress resistance [37], especially salt stress resistance. Tomato JUN-GBRUNNEN1 directly binds to the promoters of SlDREB1, SlDREB2, and SlDELLA, increasing the drought tolerance of tomato [38]. PtrNAC72 is a repressor of putrescine biosynthesis in Poncirus trifoliata and may negatively regulate drought stress responses by regulating putrescine-related reactive oxygen homeostasis [39]. Since the NAC gene family plays a crucial role in many developmental processes and responses to abiotic stresses, it is of great significance to study the NAC gene family in Theobroma cacao. In this study, we analyze the genetic structure, conserved motifs, chromosome loc...