To investigate the correlation between subnucleolar structure and function, the precise distribution and configuration of nucleolar DNA during the cell cycle of Allium sativum were determined using the NAMA-Ur DNA-specific staining technique. We showed that nucleolar DNA is present in two forms: compacted chromatin clumps and a decondensed DNA cloud. The form of the DNA within the nucleolus varied greatly as the cell cycle progressed. During telophase, chromosomes extended into the prenucleolar body. In early G1 phase, DNA was only located in the fibrillar centers in the form of the condensed chromatin clump, while in mid-G1, S and G2 phases, the two forms of DNA were distributed in the fibrillar centers (FC) and dense fibrillar component (DFC). In prophase of mitosis, nucleolar DNA, along with FC and DFC, was linked into a network structure and condensed into a large chromatin clump. The area of the DNA cloud in the dense fibrillar component changed during different phases of the cell cycle. Our results demonstrated that the configuration of nucleolar DNA undergoes a series of decondensations and condensations during the cell cycle to fulfill the function of the nucleoli during the different phases.