As in Turkey, pepper is among the most widely produced and consumed plant species worldwide. Plant nutrients and fertilization programs have significant effects on seed yield and quality of peppers. Therefore, this study was conducted to investigate the effects of effective microorganism (EM) treatments and nitrogen fertilization on seed yield and quality parameters of peppers. Kandil Dolma and Yalova corbaci pepper cultivars commonly grown in Turkey were used as the plant material of the experiments. Three different EM treatments (0, 2 and 3 L da(-1) EM) with and without N fertilizer were used. The greatest seed yield of both cultivars (68.57 kg da(-1) in Kandil Dolma and 94.90 kg da(-1) in Yalova corbaci) were obtained from 3 L EM + 2.60 kg da (-1) N treatments. EM treatments increased germination ratio of Yalova corbaci, but the differences in mean germination times were not found to be significant. Germination index, an indicator of seed performance, increased with EM treatments in both cultivars.