Function/location of menaquinone (MQ) was studied in the photosynthetic reaction center of Heliobacterium (Hbt.) modesticaldum (hRC), which is one of the most primitive homodimeric type I RCs. The spin-polarized electron paramagnetic resonance signals of light-induced radical pair species, which are made of oxidized electron donor bacteriochlorophyll g (P800(+)) and reduced menaquinone (MQ(-)) or iron-sulfur cluster (F-x(-)), were measured in the oriented membranes of Hbt. modesticaldum at cryogenic temperature. The spectral shape of transient electron spin polarized signal of P800(+)F(x)(-) radical pair state varied little with respect to the direction of the external magnetic field. It suggested a dominant contribution of the spin evolution on the precursor primary radical pair P800(+)A(0)(-) state with the larger isotropic magnetic exchange interaction J than the anisotropic dipole interaction D. The pure P800(+)MQ(-) signal was simulated by subtracting the effects of spin evolution during the electron transfer process. It was concluded that the J value of the P800(+)MQ(-) radical pair is negative with an amplitude almost comparable to vertical bar D vertical bar. It is in contrast to a positive and small J value of the P700(+)PhyQ(-) state in photosystem I (PS I). The results indicate similar but somewhat different locations/binding sites of quinones between hRC and PS I.