Abstract The invention of chromosome conformation capture (3C) techniques, in particular the key method Hi-C providing genome-wide information about chromatin contacts, revolutionized the way we study the three-dimensional organization of the nuclear genome and how it affects transcription, replication, and DNA repair. Because the frequency of chromatin contacts between pairs of genomic segments predictably relates to the distance in the linear genome, the information obtained by Hi-C has also proved useful for scaffolding genomic sequences. Here, we review recent improvements in experimental procedures of Hi-C and its various derivatives, such as Micro-C, HiChIP, and Capture Hi-C. We assess the advantages and limitations of the techniques, and present examples of their use in recent plant studies. We also report on progress in the development of computational tools used in assembling genome sequences.