In Mali and Burkina Faso, pepper yellow vein disease (PYVD) is associated with the Africa monopartite begomovirus Pepper yellow vein Mali virus (PepYVMLV). In January 2012 and August 2013, severe yellowing, leaf curling and deformation symptoms, resembling those of PYVD were observed on pepper (Capsicum spp.) across Côte d'Ivoire. Twenty leaf samples from pepper plants with symptoms were collected and tested for the presence of begomoviruses using a PCR assay with a set of degenerate primers designed to amplify the coat protein gene of Old World begomoviruses. PCR products of the expected size were obtained from seven samples, suggesting the presence of Old World monopartite begomoviruses. PCR-positive samples were further processed and viral genome sequences were amplified from three samples by rolling-circle amplification, cloned using the restriction enzyme BamHI and sequenced. The three genome sequences were 2,786 nucleotides in length and showed the highest pairwise sequence identity, 98 to 99%, with PepYVMLV isolates from Burkina Faso and Mali. A maximum-likelihood phylogenetic tree constructed with publicly available begomovirus genome sequences, confirmed the genetic relationship of the Côte d'Ivoire isolates of PepYVMLV with isolates from neighbouring Burkina Faso and Mali. To our knowledge, this is the first report of PepYVMLV associated with PYVD in Côte d’Ivoire. Our results confirm the geographical distribution of PepYVMLV in West Africa and the close genetic relationship of this viral population.