The interspecies relationships within Actinidia remain controversial due to lack of sufficient taxon sampling and molecular markers. Intergenic spacers (IGS) in the chloroplast genome have been shown to yield substantial variability and were successfully used in phylogenetic study in diverse plants. Hence, in this study, we develop IGS markers by comparing the available chloroplast genomes of Actinidia to explore the interspecific relationships within Actinidia. A total of 46 species were sampled, and three phylogenetic analyses methods (MP, ML and Bayesian) were used. Compared to the plastomes of other congeneric species, twenty-four highly variable intergenic spacers are identified, and four intergenic spacers with high polymorphism [ndhF-rps32, ndhC-trnV (UAC), rps16-trnQ (UUG) and trnE (UUC)-trnT (GGU)] were used to reconstruct phylogenetic relationships within Actinidia. The phylogeny reveals two main groups within Actinidia, and the four traditionally recognized sections are not monophyletic. Two sections (Leiocarpae and Maculatae) can be proposed, among which Leiocarpae is the earliest diverged lineage in the genus. As compared to previous work, our study provides a robust phylogenetic hypothesis that aids in our understanding of the interspecific relationships of Actinidia. Several closely related species are placed in disparate parts of the phylogeny. Moreover, the same species sampled at least two varieties are polyphyletic in our cpDNA trees, which suggests frequent hybridization/introgression events occurred in the genus of Actinidia.