Improving the poor resistance to environmental stress and the weak development of roots system in the cherry (Prunus) rootstock ‘Gisela 6’ (Prunus cerasus × Prunus canescens) is of great importance for sustainable sweet cherry (Prunus avium) production. Although a stable genetic transformation system has been developed for ‘Gisela 6’ rootstock, there is little information on the identification of genes involved in stress resistance. Using the cherry rootstock cultivar Gisela 6, we identified a total of 12 novel mitogen-activated protein kinase (MAPK) genes, designated PcMPKs. Phylogenetic analysis revealed that the PcMPKs could be divided into four groups, designated A, B, C, and D. In addition, an intron–exon structure analysis for the PcMPKs was conducted to help further understand the structure–function relationships within the cherry family. The expression profiles of PcMPKs in response to abiotic and biotic stresses were characterized using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Five PcMPKs (i.e., PcMPK4-1, PcMPK4-2, PcMPK3, PcMPK6, and PcMPK18) exhibited differential expression, and suggested their potential roles in plant responding to various stresses. This study provides the basis for further analysis on the physiological functions of PcMPKs in environmental tolerance in cherry rootstocks.