Hydroxyapatite nanoparticles (HAP NPs) are one of the widely used biocompatible materials. However, information about the reaction between HAP NPs and microorganisms is insufficient. This paper aims to understand the antibacterial property of anew nanocomposite consisting of gold-coated HAP and alginate polymer (namely, Au-HAP@Alg NPs). To the best of our knowledge, we reported the first information regarding to MIC (25 mg/mL), DIZ (no visible zone), and IC50 (0.5 mg/mL) of Au-HAP@Alg NPs toward the microorganism Escherichia coli TOP10. The real-time gene expression levels of polA, polB, cyd, mdoG, GAPDH, and 16S rRNA were maintained at stable levels up until conditions of 2.5 mg/mL Au-HAP@Alg NPs. The results showed that 16S rRNA can be a good reference under these conditions. The expressions of GAPDH, cyd, and mdoG were inhibited obviously under condition of 10 mg/mL of Au-HAP@Alg NPs. Our results indicated that the possible antibacterial mechanism of Au-HAP@Alg was through the interaction with these carbohydrate and cell wall-related genes. This novel biocompatible and antibacterial material can potentially be applied in medical and environmental fields. (C) 2013 Elsevier B.V. All rights reserved.