Actinidiaceae is a well-known economically important plant family in asterids. To elucidate the chloroplast (cp) genome evolution within this family, here we present complete genomes of three species from two sister genera (Clematoclethra and Actinidia) in the Actinidiaceae via genome skimming technique. Comparative analyses revealed that the genome structure and content were rather conservative in three cp genomes in spite of different inheritance pattern, i.e.paternal in Actinidia and maternal in Clematoclethra. The clpP gene was lacked in all the three sequenced cp genomes examined here indicating that the clpP gene loss is likely a conspicuous synapomorphic characteristic during the cp genome evolution of Actinidiaceae. Comprehensive sequence comparisons in Actinidiaceae cp genomes uncovered that there were apparently heterogenous divergence patterns among the cpDNA regions, suggesting a preferred data-partitioned analysis for cp phylogenomics. Twenty non-coding cpDNA loci with fast evolutionary rates are further identified as potential molecular markers for systematics studies of Actinidiaceae. Moreover, the cp phylogenomic analyses including 31 angiosperm plastomes strongly supported the monophyly of Actinidia, being sister to Clematoclethra in Actinidiaceae which locates in the basal asterids, Ericales.