We examined the impact of the earthquake and tsunami following the 2011 off the Pacific coast of Tohoku earthquake on the deep-sea benthic ecosystems based on radionuclide and benthic foraminiferal analysis of core sediments, collected from 3200 and 3600&thinsp;m water depths 5 and 17 months after the earthquake. Radionuclide analysis of the excess ²¹⁰Pb, ¹³⁴Cs, and ¹³⁷Cs indicated that some of the analyzed sediment core recorded deposits before the earthquake, event deposits just after the earthquake, and deposits after the Fukushima Daiichi Nuclear Power Plant accident, which caused the release of a large amount of radioactive material 4 days after the earthquake. <i>Uvigerina senticosa</i>, <i>Chilostomella oolina</i>, and <i>Elphidium batialis</i> were the dominant species in the study area prior to the earthquake. In core 4W-2012, the original or pre-earthquake assemblage layer was covered by 5-cm-thick event deposits following the earthquake that contained a high diversity allochthonous foraminiferal assemblage. Following the episodic deposition, foraminiferal density drastically decreased and many species disappeared, resulting in a decrease in species diversity. Above 10&thinsp;cm depth in the sediment, living specimens of opportunistic and competitive species gradually increased toward the sediment surface and became dominant in the top 1&thinsp;cm of the core. Thus, the episodic deposition resulting from the earthquake caused a drastic decrease in the original benthic foraminifera and colonization of opportunistic species with a low diversity within 17 months. Although there were differences in vertical change in the radionuclides and benthic foraminifera between sites, faunal change may have already occurred 5 months after the earthquake.