Anthracnose decay is one of the major causes of postharvest losses of avocados (Persea americana), during marketing. Currently, Prochloraz® fungicide is used to control anthracnose at postharvest stage which poses threat to consumer safety. Therefore, this study evaluated the effects of high and low molecular weight chitosan on the control of avocado anthracnose and fruit defence mechanism. In curative inoculation, avocados ‘(Fuerte’) were inoculated via the wounds with C. gloeosporioides spore suspension (20 μL, 1 × 106 spores mL−1). Thereafter coated with different concentrations (0.5%, 1% and 1.5%) of low (LMWC) and high molecular weight (HMWC) chitosan and fruits were held at 25 °C for 5 days. The % anthracnose incidence in avocado fruits was recorded on day 5. During preventative inoculation, wounded fruits were dipped in different concentrations of LMWC or HMWC solutions, and subsequently inoculated with C. gloeosporioides suspension. Preventatively inoculated fruits were stored for 28 days at 6.5 °C, 85% RH and thereafter for 5 days at 25 °C and 75% RH to simulated market shelf condition. The % anthracnose incidence was recorded on day 5. Fruit treated with Prochloraz® and water were included as controls for both curative and preventative infected fruits. Promising chitosan coatings with the lowest anthracnose incidence and the controls were investigated for skin epicatechin content, defence-related genes; phenylalanine ammonia lyase (PAL), lipoxygenase (LOX), fatty acid elongase (avael) and desaturase (avfad 12–3), chalcone synthase (CHS) and flavonol synthase (FLS) using RT- qPCR method. The zeta potential of selected chitosan coatings was done following standard procedures. Percentage of anthracnose incidence were lowest in 1.5% LMWC (18%, 3 mm) compared to Prochloraz® (23%, 5 mm) and the untreated fruit (90%, 24 mm). The 1.5% LMWC had the highest up-regulation of PAL, avfael, avfad 12–3, CHS, FLS genes and down-regulation of LOX gene with concomitant increase in epicatechin content (340 mg kg−1) relative to other chitosan treatments, untreated and Prochloraz® treated fruits. The superior positive zeta potential of LMWC 1.5% coating corroborates its effectiveness in controlling avocado anthracnose than HMWC 1.5%. It is possible that the interaction between the positively charged chitosan amino group (-NH3+) and the negatively charged microbial cell membrane is responsible for the enhanced antifungal activity. In late season naturally infected fruits dipped in 1.5% LMWC, anthracnose incidence dropped to 28% while Prochloraz® treated fruits showed anthracnose incidence of 82% on day 8 at the market shelf. LMWC 1.5% can replace the currently used Prochloraz®.