A real-time PCR-based detection method was developed for the root-knot nematodes (RKNs) Meloidogyne incognita and M. hapla in andosol. Different numbers of second-stage juveniles (J2) were artificially added into 20 g of soil not containing M. hapla and M. incognita and then DNA was extracted from the soils. There were significant correlations (r² = 0.8857, P < 0.05 in M. incognita and r² = 0.9978, P < 0.01 in M. hapla) between the threshold cycle (Ct) values and the number of nematodes added. Next, soils were collected at transplanting time from different sites (12 plots) in a field naturally infested with M. incognita and M. hapla to measure the initial population densities. RKNs were distributed heterogeneously in the field: the initial population ranged from 0 to 24 J2/20 g soil with the Baermann method, while that of M. incognita and M. hapla from 0.6 to 713 J2 equivalent (J2eq)/20 g soil and from 0.0 to 115 J2eq/20 g soil, respectively, with the real-time PCR method. The yield was determined by the sum of commercial sized eggplants harvested for 3 months of the cultivation period. The yield decreased in the plots with an initial population of RKNs more than 2 J2/20 g soil with the Baermann method. In real-time PCR, the yields were low in the plots with the sum of initial M. incognita and M. hapla more than 128 J2eq/20 g soil. The present study established a quantification method with real-time PCR for M. incognita and M. hapla in andosol and evaluated the relationship between the initial population of Meloidogyne spp. and the yield of eggplant.