Vanilla planifolia is the orchid species cultivated to produce the world's most popular natural flavor. Despite its economic importance, this species has long lacked the genomic resources that are decisive in modern diversity studies and breeding programs. Though, several attempts were made recently to reconstruct its 4.09 Gb diploid genome composed of 16 chromosomes pairs. While the first two attempts to reconstruct this genome brought a better understanding of some of its characteristics such as genes (approx. 59,000 protein-coding genes) and repeats content (72% of the sequence), none of these succeeded in reconstructing the entire sequence. The most complete assembly was only 82% of the expected size and only one-third of its sequence was anchored on a total of 14 pairs of pseudo-chromosomes instead of 16. In addition to frequent aneuploidy and a high rate of repeated elements, the main cause of the difficulties encountered seems to be the phenomenon of partial endoreplication, specific to the orchid family in plants. This phenomenon, which appears to be evolutionarily conserved, involves several replication rounds of a fraction of the genome - fraction that varies according to the species studied - without cell division. Despite its incompleteness, this assembly has provided valuable support for genetic mapping endeavors and the identification of Quantitative Trait Loci associated with resistance to Fusarium oxysporum. Thus allowing the discovery of candidate genes for this resistance. Most recent efforts, supported by an informed choice of the tissue to work with and a combination of technological and methodological advances, are finally leading to a complete and more contiguous assembly of this complex genome. This assembly and its refined annotation – and, more generally, the recent increase of Vanilla related omics data - should offer new opportunities in several fields such as Vanilla diversity study and varietal improvement programs, among others.