Abstract Begomoviruses (family Geminiviridae ) have a circular, ssDNA genome encapsidated in twinned icosahedral particles. Numerous begomoviruses infecting noncultivated malvaceous plants have been described, and evidence suggests that they may have given rise to some of the viruses currently found in crop plants. Here we describe an atypical begomovirus infecting ornamental Turk's hat plants ( Malvaviscus arboreus , Malvaceae). Total DNA was extracted, and the viral genome was amplified by rolling‐circle amplification (RCA), cloned and sequenced. Sequence and phylogenetic analyses indicated that the virus corresponds to a new begomovirus phylogenetically related to other malvaceous‐infecting begomoviruses from Brazil, and for which the name malvaviscus yellow mosaic virus (MvYMV) is proposed. M. arboreus plants inoculated with MvYMV infectious clones showed bright yellow mosaic and the virus progeny was identical to the isolate inoculated, thus fulfilling Koch's postulates. Strikingly, MvYMV has a nanovirus/alphasatellite‐like nonanucleotide sequence (5′‐TAGTATTAC‐3′). Moreover, a short sequence located 5′ of the nonanucleotide potentially forms a minor hairpin structure embedded in the major hairpin. Intramolecular interactions involving the sequence of the atypical hairpin structure were predicted and functional analyses were conducted to assess its biological relevance, revealing that the MvYMV Rep protein recognises this unique replication origin but not the typical begomovirus origin. Thus, MvYMV is a begomovirus with an atypical origin of replication and naturally found in noncultivated malvaceous plants.