As part of an ongoing study to understand the diversity of the badnavirus complex, responsible for the cacao swollen shoot disease in West Africa, evidence was found recently of virus-like sequences in asymptomatic cacao plants. The present study exploited the wealth of genomic resources in this crop, and combined bioinformatic, molecular, and genetic approaches to report for the first time the presence of integrated badnaviral sequences in most of the cacao genetic groups. These sequences, which we propose to name eTcBV for endogenous Theobroma cacao bacilliform viruses, varied in type with each predominating in a specific cacao genetic group. Additionally to the viral insert of type VI first identified, we recently described, with the help of Oxford Nanopore technology, a viral insert of type I and a viral insert of type III. A diagnostic multiplex PCR method was developed to identify the homozygous or hemizygous condition of the specific insert of type VI, which was inherited as a single Mendelian trait. These data suggest that these integration events occurred before or during the species diversification in Central and South America, and prior to its cultivation in other regions. Such evidence of integrated sequences is relevant to the management of cacao quarantine facilities, and may also aid novel methods to reduce the impact of such viruses in this crop.