‘Suzhouqing’ is a unique landrace of nonheading Chinese cabbage [Brassica rapa var. chinensis (Linnaeus) Kitamura] with a long history of cultivation in Suzhou of Jiangsu Province, China. However, transitional and overlapped morphologic traits make it difficult to authenticate this accession from other nonheading Chinese cabbages. Genetic relationship between ‘Suzhouqing’ and the related 10 popular accessions in the Yangtze River Delta were analyzed using two well-studied single-copy nuclear genes—ARGONAUTES 7 (AGO7) and BcMF15; the molecular identification of ‘Suzhouqing’ was determined based on the intersimple sequence repeat–sequence-characterized amplified region (ISSR-SCAR) marker. The results indicated that ‘Suzhouqing’ could be identified specifically from the other 10 accessions based on 21 specific nucleotide variations of the AGO7 gene. Sequence variations show a strong correlation with leaf morphology, suggestive of partial causal links between the two. Genetic relationship analysis showed that five accessions with close geographic locations had a very close genetic relationship, whereas the genetic relationship of the other five accessions was related to their morphologic similarity. One exception, ‘AJH’, might undergo a special evolutionary process. Furthermore, ISSR-880 was screened as the specific primer to identify accession ‘Suzhouqing’, and a specific discrimination ISSR-SCAR marker was explored, which amplified no target band in any other accessions. The development of molecular markers for the specific identification of ‘Suzhouqing’ in 11 popular accessions in the Yangtze River Delta could provide a theoretical basis for the protective identification of other agricultural crops.