Resistance of Alternaria alternata to boscalid, the first succinate dehydrogenase inhibitor (SDHI) fungicide labeled on pistachio, has become a common occurrence in California pistachio orchards and affects the performance of this fungicide. In this study, we established the baseline sensitivities of A. alternata to the new SDHIs fluopyram, fluxapyroxad, and penthiopyrad and assessed their cross resistance patterns with boscalid. Examination of the effective fungicide concentration that inhibits mycelial growth to 50% relative to the control (EC50) for 50 baseline isolates revealed that the majority were sensitive to boscalid, penthiopyrad, fluopyram, and fluxapyroxad. Analysis of EC50 values for boscalid for 117 A. alternata isolates originating from boscalid-exposed orchards showed that 44, 3, 1, and 69 isolates had sensitive, reduced sensitivity, moderately resistant, and highly resistant boscalid phenotypes, respectively. Molecular investigation of the occurrence of known SDH mutations showed that, among the 69 isolates highly resistant to boscalid, 44, 2, 14, and 1 isolates possessed the mutations leading to the H277Y, H277R, H134R, and H133R amino acid substitutions in AaSDHB, AaSDHB, AaSDHC, and AaSDHD subunits, respectively. Some SDHB or SDHC mutants displayed highly sensitive, sensitive, or reduced sensitivity phenotypes toward penthiopyrad or fluxapyroxad, whereas other had low, moderate, or high levels of resistance to these fungicides. In contrast, all the SDHB mutants were sensitive to fluopyram, while 10, 5, and 1 SDHC mutants had sensitive, reduced sensitivity, and moderately resistant fluopyram phenotypes, respectively. The SDHD mutant had reduced sensitivity to fluopyram and penthiopyrad but was highly resistant to fluxapyroxad. The discrepancies of cross-resistance patterns between SDHIs suggest that their binding sites in complex II may differ slightly and that additional mechanisms of resistance to these compounds are likely involved. Ultimately, the findings of this study should lead to the rational and sustained deployment of new SDHIs in Alternaria late blight spray programs.