The pigeon pea cyst nematode, Heterodera cajani, is an economically important plant-parasitic nematode in sesame production. The objective of the study was to investigate distribution of H. cajani in the major sesame producing areas in Myanmar. Before cultivation, soil samples were collected in 96 local farmer’s fields: (19 fields in Magway, 20 fields in Mandalay, 14 fields in Sagaing and 43 in Nay Pyi Taw), and nematode density was quantified by real-time PCR. The cyst nematode was detected in 63.2% of the fields in Magway and the mean density was 22.6 eggs equivalent (20 g soil)−1. In Mandalay and Nay Pyi Taw, the cyst nematode was detected in 40.0% and 18.6% of the fields with the mean densities of 9.9 and 21.0 eggs equivalent (20 g soil)−1, respectively. By contrast, the cyst nematode was not detected in Sagaing fields, in which sesame is rotated with paddy rice. Infestation of root-knot nematodes (RKN, Meloidogyne spp.) was also evaluated, because sesame is generally rotated with rice and pulses, which are attacked by RKN. The results showed 25.6% infestation of RKN with a mean density of 34.3 eggs equivalent (20 g soil)−1 only in Nay Pyi Taw, while there was no infestation in Magway, Mandalay, and Sagaing. The relationships between the nematode infestation level and the cropping patterns in each sesame growing area in Myanmar were discussed.