This study investigates the combustion instability of a compression ignition engine using dynamical system analysis in the form of a recurrence plot approach. In-cylinder combustion chamber pressure and crank angle are obtained from a six-cylinder, turbocharged diesel engine with a common-rail direct fuel injection system using a piezoelectric transducer and encoder, respectively. The common-rail system keeps the fuel pressure at a constant rate, which helps to minimise the effect of fuel pressure in this study. Constant speed and 4 loads are investigated. The engine emission and operation can be influenced by combustion instabilities and inter-cycle variability. Previous studies reported that ambient temperature, fuel pressure and injection timing, residual gases and fuel properties significantly alter the combustion instability. This study focus on the effect of biodiesel on this phenomena. Considering the CI engine as a dynamical system, the dynamic state of the combustion can indicate its stability. Typically, peak pressure, heat-release rate and indicated mean effective pressure in a range of consecutive cycles are utilised to represent the variability of combustion. The recurrence plot of these data is used to visually study the characteristics of combustion dynamics. Additionally, the recurrence quantitative analysis is used to present the characteristic dynamics of the system. The study finds that the combustion instability is higher for biodiesel compared with diesel, owing to the fuel properties. The results aid in developing our understanding of the complexity of biodiesel combustion in a modern engine and help to advance the combustion control strategy in order to improve the performance of biodiesel fuelled engines