Rose belongs to Rosaceae family is the most important ornamental plant having 30% share in overall floriculture market. However, limited molecular studies have been conducted for rose in past and its available genetic resources are also poor. We constructed database containing 35,385 transcripts and 2,353 known and /or novel flower specific miRNA from three rose cross-species (Rosa x hybrida Vital, Marcia and Sympathy) and Rosa rugosa (Haedang) by using deep-sequencing method. Profiles of miRNAs were analyzed collectively and species specifically to evaluate the abundance of miRNAs. The miRNA target genes identified in cross-species can interpret role of miRNAs, in spite of missing miRNA targets in corresponding rose because of small number of reads. Based on these evidences, most commonly abundant miRNAs in 4 rose subspecies flowers are targeted to various transcription factors (TFs) involved in flower development such as AP2-domain containing TF (miR172), SPL9 (miR178) and SCL6 (miR176). In addition, we focused on miRNAs abundant in Marcia and found that the targets of these miRNAs are involved in carotenoid, flavonoid and phenylpropanoid biosynthesis pathways. Statistically significant abundance of miRNAs in these pathways suggests the regulatory role of these miRNAs over white coloring of Marcia flowers. These studies depict the significance of this database to expand our knowledge of genetic control of rose flower development and their different phenotypes.