Silver nanoparticles (AgNPs) are one of the most widely used nanomaterials, although the mechanisms of AgNP toxicity in terrestrial plants is still unclear. We compared the toxic effects of AgNPs and AgNO3 on Brassica nigra seed germination at physiological and molecular levels. Both AgNPs and AgNO3 inhibited seed germination, lipase activity, soluble and reducing sugar contents in germinating seeds and seedlings. These reductions were more pronounced in AgNP treatments than AgNO3 treatments. Application of 200–400mg/L both AgNPs and AgNO3 increased transcription of heme oxygenase-1. However, at 800, 1600mg/L, AgNPs or AgNO3 suppressed HO-1 expression. At 400mg/L, AgNPs or AgNO3-induced inhibitory effects on seed germination and were ameliorated by the HO-1 inducer, hematin, or NO donor, sodium nitroprusside (SNP). Additionally, 4μM hematin and 400μM SNP were able to markedly boost the HO/NO system. However, the addition of the HO-1 inhibitor (ZnPPIX) or the specific scavenger of NO (cPTIO) not only reversed the protective effects conferred by hematin, but also blocked the up-regulation of HO activity. In addition, hematin-drived NO production in B. niger seeds under AgNPs was confirmed. Our results at physiological and molecular levels suggested that AgNPs were more toxic than AgNO3. Based on these results, for the first time, we suggest that endogenous HO is needed to alleviate AgNPs-induced germination inhibition, which might have a possible interaction with NO.