The present study is aimed at comparing the fatty acid profiles, cholesterol, and atherogenicity index of Bactrian and dromedary camel meat by using discriminant analysis to identify the more discriminating fatty acids. Six muscles were sampled from nine Bactrian and nine dromedary camels and analyzed for fatty acid parameters and cholesterol content. The mean fatty acid profiles differed in higher proportion between species than between muscles. The main discriminating fatty acids between species (100% well-classed samples) were C15:0, C17:1, C14:1, C20:0, and C18:0. A significant difference was also observed in cholesterol content, with more cholesterol in Bactrian meat (53.6 ± 12.5 mg/100 g) compared to dromedary meat (49.4 ± 11.2 mg/100 g). However, the atherogenicity index was lower in Bactrian meat (1.196 ± 0.148) than in dromedary meat (1.379 ± 0.109). Despite the dietetic interest in camel meat due to its low cholesterol and low-fat content, the high atherogenicity index compared to other red meat appeared as an unfavorable argument.