In recent years, the long-grain shape has been found as a new desired quality trait in the breeding of rice in China. The SLG7 gene is a novel gene responsible for slender grain shape in rice. So far, not much information is known regarding the functional molecular markers of SLG7. In this study, a functional marker M-SLG7 for the 11-bp deletion of promoter region of SLG7 was developed. Specificity and applicability of the marker were verified by 60 core breeding accessions and two breeding populations. The accessions, which possessed the SLG7 allele with 11-bp deletion in the promoter region, had longer grain length and better quality. Here, we recommend the use of the simple, inexpensive assay for routine genotyping of slender grain and lower chalkiness in the breeding population for discrimination of SLG7 genotype in rice germplasm.