To identify the differences among hybrid lines from ‘MB09’בLongshu 7’ in DNA level and cytogenetical level,we used parent materials as contrast,and analyzed DNA fingerprint characteristic of 20 excellent hybrid lines (F₁ clone generation) with SSR molecular marker technology,and the pollen fertility and chromosome configuration at meiosis metaphase Ⅰof pollen mother cells (PMCMⅠ) of 8 selected outstanding hybrid lines (F₁ clone second generation) with regular slide-preparing technique and microscopy examination method,which could provide for hybrid breeding of excellent potato strains on the basis of the molecular cytology.The result showed that:(1) two suitable SSR primers C57 and S25 were screened for fingerprint establishment,and a SSR fingerprint was obtained by PCR amplification,which could identify 20 hybrid lines and their parents;(2) the pollen fertility rate of hybrid excellent lines 1,2,7,11,13,14,15 and 20 ranged from 36.73% to 87.08% in addition line F_1-7(87.08%) was the highest and significantly higher than the parent(83.33%),which had some differences;(3) chromosome configurations at PMCMⅠ of the 8 hybrid lines were obviously different,which include univalent,bivalent,trivalent and quadrivalent ,and the bivalent rate of 8 hybrid excellent lines ranged from 49.13% to 82.91% and line F_1-7 was the highest.The study illustrated SSR fingerprint character for 20 good potato hybrid lines and differences of pollen fertility and chromosome configuration for 8 excellent lines.