This second and final instalment of the conference report from International Congress on Infectious Diseases 2014 follows on from part one, published in Future Microbiology (volume 9/issue 11). The 16th International Congress on Infectious Diseases was held in Cape Town this year, marking the return of the conference to Africa for the first time in 22 years. While infectious diseases such as malaria, tuberculosis and HIV--all still prevalent in the African healthcare landscape--dominated the program, the conference featured several important sessions on fungal infection and a significant number of posters devoted to this critical medical area. Within the context of the rise of antimicrobial resistance, now identified by WHO as one of the three greatest threats to human health, came the message that resistance is not limited to antimicrobials, but that antifungal resistance is also a significant and emerging threat worldwide.