Anthocyanins are important molecules that are responsible for fruit color formation and are also beneficial to human health. To date, numerous structural and regulatory genes associated with anthocyanin biosynthesis in peach (Prunus persica) have been reported based on linkage analysis. In this study, we sought to identify further genes associated with anthocyanin content in peach by conducting a genome-wide association analysis of 129 peach accessions to detect markers associated with the trait. Significant association signals were detected when anthocyanin content was considered a qualitative character but not when it was considered a quantitative trait. We detected an association region located between 11.7 and 13.1 Mb in chromosome 1, a region in which only 133 of 146 genes have previously been functionally annotated. Gene ontology annotation of the genes in this region showed that membrane-associated genes (including one gene encoding a chloride channel protein and 17 sugar transport/carrier-associated genes) were significantly enriched, and we focused on these in subsequent analyses. Based on in vitro induction of anthocyanins in fruit flesh using different exogenously applied sugars and subsequent culture, we found that the expression level of 3 of the 18 membrane-associated genes, Prupe.1G156300, Prupe.1G156900, and Prupe.1G157000, increased during induction treatment. Furthermore, during the fruit development period of a white-fleshed and a red-fleshed peach cultivar, the expression of one gene encoding a transmembrane sugar transport protein was observed to be positively correlated with anthocyanin biosynthesis. These results will facilitate understanding of the molecular mechanism of anthocyanin biosynthesis in peach.