Aims: There has been an increasing number of pathogens becoming resistant to multiple classes of antibiotics. The study on how mutation emerges is therefore crucial to promote further understanding in this area. Conventional methods for such studies involve the monitoring of growth by standard plate count and biomolecular sequencing. This is however tedious and not cost effective. The aim of this paper is thus to introduce a novel system that enables real-time monitoring of bacterial 'mutation-in-progress'. Methods and Results: This system provides real-time data, thus enabling confirmatory and further work to be performed at the important points when mutation is initiated. The system integrates spectroscopic techniques as the detection system and various supporting systems, such as a nutrient replenishing system, a pH control system and a waste system to allow for extended monitoring. In this paper, the feasibility of monitoring the emergence of ciprofloxacin resistance in Staphylococcus aureus was demonstrated as an initial example. The integrated system was found to require significantly less material resource and manpower compared with conventional techniques. Conclusions: The novel system to monitor bacterial mutation-in-progress is presented. The work reported herein demonstrates such a system to be effective and efficient in performing real-time monitoring of mutation-in-progress, especially in extended time frames for mutation into the weeks and months. Significance and Impact of the Study: With the successful optimization of this system, researchers can learn about the dynamics of antibiotic resistance and further understand how the mutation of bacteria occurs.