Background: Calcium-dependent protein kinases (CDPKs) play important roles both in developments and response to stresses, via mediating Ca2+ signal transduction in plants. To characterize the CDPKs in apple (Malus domestica), the apple CDPK gene family, together with those from pear (Pyrus bretschneideri), peach (Prunus persica), strawberry (Fragaria vesca), and and Arabidopsis thaliana, were analyzed at the genome-wide level in the present study.Results: A total of 116 CDPKs, consisting of 24 MdCDPKs, 28 PbCDPKs, 16 PpCDPKs, 14 FvCDPKs, and 34 AtCDPKs, was identified from apple, pear, peach, strawberry, and Arabidopsis, respectively. An integrated analysis of these CDPKs was performed on their chromosomal distribution, phylogenetic and collinearity relationships, characteristics of gene structures and conserved motifs. As a result, the CDPK gene family members were showed to be highly conserved both at their kinase and EF-hand domains. Among 209 gene-pairs with interspecies collinearity, there existed 22, 36, 21, and 25 ones between MdCDPKs and other CDPKs in Arabidopsis, pear, strawberry, and peach, respectively. And the evaluated Ka/Ks ratios were less than 1 between the CDPK gene pairs with collinearity relationships. Transcriptomic analysis demonstrated that among 24 members of the apple CDPK gene family, two up-regulatory ones (HF05266 and HF09216) and two down-regulatory ones (HF05471 and HF15429), were differentially expressed with significance between the apple fruit developmental stage S4 (mature) and other stages (early growing-S1, mid growing-S2, and late growing-S3), respectively.Conclusions: The whole genome duplication and subsequent purifying selection, might have played an important role in the CDPK gene expansion, leading to structural and functional novelty during evolution of the species lineages. In many cases, the MdCDPK genes within a phylogenetic group could show the different expression patterns at the transcriptional level, suggesting that these MdCDPKs have undergone genetic variant events and potential functional diversification. Some of MdCDPKs with significantly differential expression, were indicated their particular functions at the specific stages of apple fruit development.