Control of the two spotted spider mite, Tetranychus cucurbitacearum (Sayed) using conventional acaricides resulted in many problems. Thus, this study aimed to evaluate the effect of silica nano-particles (SiNPs) as a new approach to control spider mite on soybean plants. Three concentrations of SiNPs (250, 350 and 450 ppm) were sprayed on two soybean varieties, Giza 35 and Giza 111 during 2014 season. The reduction percentage in the population of the mite was recorded under field conditions. The obtained results indicated that the mean reduction percentage in mite population appeared a concentration response. The concentration of 450 ppm of SiNPs induced the highest reduction of mite on both soybean varieties Giza 111 and Giza 35, with values of 78.91% and 62.34%, respectively, followed by concentrations of 250 (71.24% and 38%) and 350 ppm (62.16% and 41.92%),respectively throughout the experimental period. The motile stages of mite T. cucurbitacearum on soybean variety Giza 111 was more susceptible to SiNPs than variety Giza 35. On the other hand, the highest values of seed yield/fed were recorded for the two varieties grown at 450 ppm in contrast with the control and250 ppm which produced lower seed yield/fed. High differences in SDS-Polyacrylamide gel electrophoresis protein profiles were found between two soybean genotypes treated with different concentrations of SiNPs. Increasing SiNPs concentration, increased changes in protein profile in both soybean genotypes. Six RAPD primers revealed low to moderate polymorphism and genetic variations among the different concentrations of SiNPs and between both soybean genotypes. The changes in DNA profiles included variation in band intensity, presence or absence of certain DNA bands and even appearance of new bands. Genomic template stability test was performed for the qualitative measurement of changes in randomly amplified polymorphic DNA profiles. This study concluded that DNA stability was affected by SiNPs concentrations of 350 and 450 ppm for both soybean varieties as identified by RAPD markers.