Objective To analyze the contents of amino acids in Paecilomyces hepiali (P. hepiali) and Tolypocladium sinenis (T. sinensis) and their nutritive values, so as to provide a basis for related researches and applications of the two kinds of fungi. Methods The mycelia of P. hepiali and T. sinensis were hydrolyzed with 6 mol·L^-1 HCl, and the amino acids from the mycelia were separated by C₁₈ reversed-phase column with gradient elution and o-phthalaldehyde-fluorenylmethyl chloroformate (OPA-FMOC) pre-column derivation using Agilent 1200 high-performance liquid chromatograph. The content of sample amino acids was determined by the peak areas ratio between the samples and standard amino acids. Results A total of 17 proteolytic amino acids from P. hepiali and T. sinensis were determined in this study. The contents of 4 kinds of amino acids (aspartic acid, valine, isoleucine and leucine) in P. hepiali were higher than those in T. inensis, while the contents of 11 kinds of amino acids (glutamic acid, serine, glycine, threonine, arginine, alanine, tyrosine, cystine, methionine, lysine and proline) in T. inensis were higher than those in P. hepiali. The total contents of amino acids, essential amino acids and non-essential amino acids in T. Sinensis were higher than those in P. hepiali, and the content of branched chain amino acids in P. hepiali was higher that in T. sinensis. World Health Organization/Food and Agriculture Organization (FAO/WHO) reference model of essential amino acids was used to evaluate the nutritional values of amino acids in P. hepiali and T. sinensis, and the results showed that the scores of ratio coefficient of amino acids in P. hepiali and T. sinensis were 92.06 and 88.17, respectively. Conclusion The contents of protein amino acids in P. hepiali and T. sinensis are different, but they both have relatively high nutritional values.