Simple sequence repeat (SSR) markers play an important role in genetic and molecular breeding programs, especially for non-model species. We identified SSRs from expressed sequence tags (EST-SSRs) and whole genome sequences (gSSRs), by analyzing the transcriptome and genome of the Mongolian sea buckthorn (Hippophae rhamnoides subsp. Mongolica) cultivar ‘Sunny’. Using the same number of loci, EST-SSRs showed higher transferability to Hippophae than gSSRs, and phylogenetic trees based on EST-SSRs demonstrated higher resolution for classifying Hippophae species and subspecies into clades, possibly due to high conservatism and/or existence of adaptive divergence between species/subspecies in coding sequence regions. In contrast, parentage analyses showed that gSSRs were more effective at resolving parentage than EST-SSRs due to higher level of polymorphism in gSSRs. The markers developed in this study can be used in the identification and pedigree reconstruction of species/subspecies of sea buckthorn, while their usage in clarifying phylogenetic relationship among species remains to be discussed. The comparison between EST-SSRs and gSSRs would provide insight into the trade-off between differentiation and polymorphism in marker selection for breeding programs.