We report the first confirmed cases of Zika virus disease (ZVD) in Kenya and provide the associated genomic sequences.The study is part of a prospective febrile illness surveillance study in Kenya.A cluster of ZVD was identified in febrile patients presenting at King Fahd Referral Hospital, Lamu Island. Clinical signs resembled those caused by dengue or malaria and included fever, chills, muscle and joint pains and headache. The Biofire Film Array Global fever panel (BioFire Diagnostics, UT, USA) identified ZIKV in 3/5 blood samples. RNA extracted from plasma was used for sequence library preparation and subsequent viral enrichment using the VirCapSeq-VERT probe set designed at the Center for Infection and Immunity (CII), Columbia University. Enriched libraries were sequenced on the NextSeq 2000 (Illumina, San Diego, CA, USA). Assembled genomes were classified into lineages and a spatio-temporal phylogeny inferred with Nextstrain v8.5.3.Assembled genomes produced contigs covering between 3,363 and 10,950 nt that mapped to the Asian lineage of ZIKV and branched with genomes from India. Mutation profiling revealed viral strains with potentially enhanced transmission and immune evasion capabilities.The presence of the more transmissible Asian lineage ZIKV that has previously caused big outbreaks of ZVD in the Americas raises significant public health concern.