Japan has reported 26 cases of coronavirus disease 2019 (COVID-19) linked to cruise tours on the River Nile in Egypt between March 5 and 15, 2020. Here, we characterized the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome of isolates from 10 travelers who returned from Egypt and from patients possibly associated with these travelers. We performed haplotype network analysis of SARS-CoV-2 isolates using genome-wide single-nucleotide variations. Our analysis identified two potential Egypt-related clusters from these imported cases, and these clusters were related to globally detected viruses in different countries. © Copyright © 2020 Sekizuka, Kuramoto, Nariai, Taira, Hachisu, Tokaji, Shinohara, Kishimoto, Itokawa, Kobayashi, Kadokura, Kamiya, Matsui, Suzuki and Kuroda.