We have generated Drosophila melanogaster lines carrying a modified genomic fragment which encodes the D. melanogaster variant H2A.F/Z class histone, His2AvD, fused to the green fluorescent protein (GFP) of the jellyfish Aequorea victoria. We show here that the fusion protein consists of functional GFP and functional histone His2AvD. The His2AvD portion of the fusion gene was shown to be functional by rescue of His2AvD mutant lethality. Fluorescence of the fusion protein in vivo was observed in embryonic cleavage stage interphase nuclei and on chromosomes as early as cycle 9, correlating with activation of transcription. Unlike transcription factors, the His2AvDGFP protein remained on transcriptionally inactive chromosomes throughout mitosis. Subsequently, fluorescence was observed in nuclei at all stages of embryonic and larval development and in adult somatic tissues, consistent with the distribution of His2AvD observed by immunohistochemical staining. This functional fusion histone acts as an excellent in vivo marker for chromosomes and chromosome behavior and, given the ability of the fusion gene to prevent null-mutant lethality, without disrupting normal cellular functions. The very high level of conservation of the H2A.F/Z family of variant histones suggests that the equivalent fusion protein construct should function equally well in a wide range of organisms.