Background: Biliary cancer are relatively rare, highly aggressive and have poor prognoses. Most biliary cancers are diagnosed in the advanced and metastatic stages. Chemotherapy is the main treatment of advanced biliary cancer. We focus on gene mutation and tumor mutation burden (TMB) of biliary cancer. Methods: We retrospectively reviewed one hundred and fifty-six cases of biliary cancer. One hundred and fifty-six tumor tissues and 35 plasma samples were subjected to next-generation sequencing (NGS), which enables simultaneously assess snv, indel, rearrangements and cnv variations at least 59 genes (range 59-1021 genes). Results: Fifty-eight patients were intrahepatic cholangiocarcinoma (IHCC), 50 were extrahepatic cholangiocarcinoma (EHCC) and 48 were gall bladder cancer (GBC). From tissue samples, the commonly mutated genes were different in three groups. TP53 was the most frequently mutated gene among the three groups (IHCC 43%, EHCC 58%, GBC 79%). KRAS (33%), TERT (16%), LRP1B (16%), IDH1/2 (10%) were usual in IHCC. KRAS (28%), SMAD4 (20%), STK11 (18%), ARID1A (12%) were usual in EHCC. And ERBB2 (19%), LRP1B (17%), TERT (15%), MLL3 (15%) were usual in GBC. TP53, LRP1B and MLL3 had a higher frequency in GBC than cholangiocarcinoma (p < 0.05), and KRAS was more common in cholangiocarcinoma than GBC (p < 0.05). 72.4% IHCC, 76.0% EHCC and 60.4% GBC had gene mutation associated with target therapies, which involved in multiple signal pathway, such as IDH1/2, FGFR, ERBB1/2/3, MET, PIK3CA, PTEN, BRCA, etc. Thirty-five patients had paired tissue and plasma samples, 21 stage Ⅲ/Ⅳ, 11 stage Ⅱ and 3 unknown. The concordance between tissue and plasma was 53% in all patients and was higher in stage Ⅲ/Ⅳ than stage Ⅱ (p < 0.05). One hundred and thirty-three tissue samples assessed TMB, the mean TMB was highest in the GBC group, followed by EHCC and IHCC (7.1 vs 5.5 vs 3.9 muts/Mb, p < 0.05). The proportion of TMB-H (defined 9.0 muts/Mb as cutoff value) was higher in GBC than IHCC and EHCC. Conclusions: IHCC, EHCC, and GBC have distinctive mutational landscapes and TMB features. It maybe guide different target therapy and immunotherapy strategies in the clinic. ctDNA has promising potential in biliary cancer.