To assess the ecological risk of the coral reef habitats of Khark and Kharko islands in the Persian Gulf, (Bushehr province), the surface sediment samples were collected from seven stations, in September 2019. The islands have a great ecological value due to the presence of coral reefs. The amounts of potentially toxic elements, sediment texture, total organic matter, total phosphorus and total nitrogen in the sediments were measured by inductively-coupled plasma mass spectrometry, sieve analysis, furnace burning method, spectrophotometer, and Kjeldahl, respectively. The mean concentrations of Al, Fe (%) and Ni, Pb, Zn, V, TP and TN (mg/kg) in the sediments were recorded 0.76±0.53, 0.55±0.35, 35±19, 2.1±1.5, 22±10, 40±25, 0.7±0.3 and 14.7±6.2, respectively. Based on the amount of Ni and Zn enrichment factors (moderate to very sever, respectively), their source around Khark Island could be related to human activities, such as oil industries. Pollution load index (0.06-0.25) showed all stations without pollution. The amount of Ni in stations 1 and 7 were higher than the "range of moderate effect" and "level of possible effects", which indicates the possible biological effects of this element on the benthic organisms. In general, the ecological quality of surface sediments around Kharko was better than Khark Island.