In 2018, a Zika infection was detected in patients in the Republic of Guinea. We determined the complete genome sequence of the Faranah/18 strain of Zika virus (ZIKV) isolated using C6/36 cells. The genome sequences are significantly different from those of other African ZIKVs. This isolate has 13 aa substitutions in nonstructural polypeptides, an additional glycosylation site on protein E, and unusual localization of MSI1 binding sites in the 3’-UTR of the African lineage. Additionally, Faranah/18 formed a separate lineage into African genotypes with divergence times near 94 and 646-861 years from Senegal and Uganda ZIKVs, respectively.