Biodiesel, an alternative diesel fuel, is made from renewable biological sources such as vegetable oils and animal fats. In Thailand, the government has promoted the use of biodiesel with the purpose to reduce the imported fuel oil, air pollution and also to reduce global warming contribution. Despite obvious benefits of this industrial development, its production process generates waste/by-product, and wastewater which could have a significant impact on the environment if they are not managed properly. This research was aimed to adopt industrial ecology measures to alleviate the environmental problems encountered in biodiesel industry in Thailand. Five biodiesel factories were selected to analyze the nature of their industrial ecosystems including clean technology options and waste exchange between biodiesel industries and other economic activities. The results showed that 1 m3 of biodiesel production generated spent bleaching earth, glycerin and wastewater equal to 8 kg, 140 kg and 0.47 m3, respectively. All generated waste/by-product can be reuse/recycle or utilized as raw material for other industry or agricultural sector. Such an approach can contribute in transforming the biodiesel industry into a more environmentally friendly industrial activity.