Background: Small cell/neuroendocrine bladder cancer (SCBC) is a rare and clinically aggressive disease. However, its molecular characteristics are poorly studied; hence, biology-based therapeutic options are not available. Strong pan-cancer similarity in gene expression signature of neuroendocrine (NE) tumors including SCBC and small cell lung cancer (SCLC) has been reported. Recent genomics studies discovered that SCLC can be grouped into lineage- specific transcription factor (TF)-defined subtypes. Therefore, we explored whether TF-defined molecular subtypes could also be observed in SCBC with the goal of developing subtype-specific therapeutic strategies. Methods: Whole transcriptome RNAseq on a cohort of n = 44 pure SCBCs collected at Johns Hopkins (n=20) and Tenon Hospital (Paris) (n=24) and DNA panel sequencing on subset of the tumors (n=24) were performed. Two expert genitourinary pathologists selected the cases for the analyses based on the histopathological characteristics of the tumor tissue. Results: SCBC tumors displayed overexpression of canonical NE markers and high mutation rates in TERT, TP53 and RB1 with 92%, 75% and 38%, respectively, confirming the concordance between genomic features and histopathologic characteristics.Lineage-specific TFs (ASCL1, NEUROD1, and POU2F3) defined three molecular subtypes of SCBC that resembled the previously reported SCLC subtypes. The three subtypes expressed variable levels of NE biomarkers and were heterogeneous with respect to distinct downstream therapeutic targets. The ASCL1 and NEUROD1 subtypes expressed the highest levels of NE lineage-specific gene expression and were associated with expression of known regulators of the neuroendocrine phenotype including FOXA2 and HES6, respectively. The ASCL1 subtype was also enriched with DLLs and other genes that control oncogenic Notch signaling, whereas tumors enriched with POU2F3, a master regulator of the NE-low SCBC subtype, expressed TRPM5, SOX9 and CHAT. Finally, an inverse association between NE lineage-specific gene expression and immune signatures associated with response to immunotherapy was observed. Conclusions: Three lineage-specific TFs (ASCL1, NEUROD1, and POU2F3) defined discrete molecular subtypes in SCBC. Each subtype was characterized by distinct therapeutic targets and gene expression signatures associated with response to immunotherapy. Future studies will be required to test the clinical relevance of these observations.