The complete mastitis control program is insufficient for the starting dairy industry country, and therefore it might cause emerging of new mastitis pathogens. This longitudinal study aimed to determine the association of the infected dynamic status of the main pathogens responsible for mastitis with seasonal variations, the proportions of transient and chronic intramammary infection (IMI) episodes, and the duration of IMI. This study was conducted on a training smallholder dairy farm in Phnom Penh, Cambodia, from January 2023 to July 2023. Trained veterinarians aseptically collected quarter milk samples from all milking cows (n = 21) every 2 weeks until the end of the study, accounting for 3–16 times of milk collection per cow based on their period of lactation. All collected milk samples (n = 812) were cultured, and subsequently, all bacterial colonies were identified using a MALDI-TOF mass spectrometer. An IMI episode is defined as a sequence of consecutive isolates of a specific bacterium from the same quarter. The duration of an episode is the time between the new IMI and its cure. Two types of IMI were defined as transient IMI and chronic IMI that lasted for 28 days or more. Results of the IMI episodes, distributions of no, single, double-mixed, and 3-mixed IMI were 61.1%, 31.9%, 6.3%, and 0.7%, respectively, in which the mixed IMI accounts for 18% of IMI samples. Streptococcus uberis, Staphylococcus chromogenes, and Streptococcus gallolyticus were the main organisms responsible for the mastitis epidemic on this farm. These bacteria had higher ratios of chronic episodes than the other mastitis bacteria found on this farm. In addition, results obtained from Cox’s model showed that S. chromogenes had a longer time to cure than pathogens other than S. uberis and S. gallolyticus, in which S. gallolyticus linked to colon neoplasia in humans. In conclusion, the lack of an optimal mastitis control program, in this case, provides information on the emerging mixed infections, emerging mastitis pathogens, and emerging chronic S. chromogenes infections.