Big fruit size and nice red pigmentation combined with good flavor should be the major target for red-fleshed kiwifruit (Actinidia spp.) breeding programs. Genetic diversity and plant characteristics were evaluated on a set of kiwifruit accessions with predominantly red flesh to identify the superior individuals for further breeding or study of commercial application. The leading phenotypic characters varied widely among the accessions. Accession R reached average fruit weight ’100 g, whereas it ranged from 43.15 to 84.71 g for the other accessions. Fruits of L and Q were flatter in shape than the others. The core volume accounted for fruit proportions ranging from 2.33% to 11.42%. ‘Chuhong’, ‘Honghua’, and K exhibited a round fruit apex, whereas most others showed a depressed apex. R, L, and Q had the highest a* values in the inner pericarp and also the most appealing visual coloration. Results revealed significantly higher soluble solid content (SSC), total sugar, and sugar/acid ratio in Q, R, and L. The 12 pairs of simple sequence repeat (SSR) markers were successfully used to characterize the genetic variability and confirm true-to-type identity for four accessions. However, the limited number of markers had no ability to discriminate among the other 11 accessions. Based on additional 28 SSRs, six of the indistinguishable accessions were confirmed to be genetically different, and three seemed to belong to the same clone vine. The results demonstrated that application of SSR data could improve the efficiency of identifying red-fleshed kiwifruit germplasm.