The recently growing interest in studying flight behaviours of fruit flies, Drosophila melanogaster, has highlighted the need for developing tools that acquire quantitative motion data. Despite recent advance of video tracking systems, acquiring a flying fly's orientation remains a challenge for these tools. In this paper, we present a novel method for estimating individual flying fly's orientation using image cues. Thanks to the line reconstruction algorithm in computer vision field, this work can thereby focus on the practical detail of implementation and evaluation of the orientation estimation algorithm. The orientation estimation algorithm can be incorporated into tracking algorithms. We rigorously evaluated the effectiveness and accuracy of the proposed algorithm by running experiments both on simulation data and on real-world data. This work complements methods for studying the fruit fly's flight behaviours in a three-dimensional environment.