Okra (Abelmoschus esculentus) is a crop of rising importance. It is mostly consumed as a vegetable, but is increasingly finding industrial and medical uses. Okra is tolerant to high temperatures and likely has the potential to adapt relatively well to climate change compared to other vegetable crops. Major current production constraints are virus diseases. Molecular markers for okra crop improvement are scarce due to the allopolyploid nature of the species. Microsatellite and single nucleotide markers developed based on transcriptome sequences have not provided the breakthrough for molecular breeding of okra. Improved markers that work effectively, also in the absence of reference sequences, and that account not only for sequence variation, but also for copy number polymorphisms, are required to support molecular breeding approaches in okra.