Nanocrystalline MnxZn1-xFe2O4 with the varying concentration of Mn (x= 0.25, 0.50) have been synthesized by citrate route method. The effect of annealing temperature on structural and magnetic properties of as-synthesized materials was studied. The X-ray diffraction (XRD) analysis revealed the improved crystallinity and purity of the samples at high temperature annealing. Also, the increase in the annealing temperature yielded nanocrystals with bigger crystallite size. The samples annealed at higher temperature were analyzed by TEM which showed the formation of irregular polycrystalline particles with average size in the range of 150-180 nm. The magnetic measurements were taken using vibrating sample magnetometer and displayed the superparamagnetic behavior of the prepared materials. Also, the increase in magnetization was observed with Mn substitution.