Main conclusion Partial male sterile mutant offers high hybrid recovery and seed set upon crossing. Partial sterility is recessive, monogenic and caused due to impairment of pollen function, which is supported by ddRAD sequencing. Finger millet, a nutri-cereal, has wider adaptability mainly grown as a rainfed crop in arid and semiarid tropics of Asia and Africa. Highly autogamous nature and small florets makes the hybridization tedious and hence the genetic improvement has been very slow. To address this, a novel partial male sterile mutant (ps1) was characterized extensively in line of its utility in hybridization breeding. An in vivo pollen study using fluorescence microscopy revealed the cause of partial male sterility in ps1 mutant as impairment of pollen germination and pollen tube growth on stigma. The mutant sets similar to 10% seeds upon bagging, 20% under open pollination and up to 49% in controlled crossing. Hybrid recovery (outcrossing) in 46 crosses with ps1 ranged from 28.6% to 81.2% with an average of 56.7% under controlled crossing. An extensive genetic study using 46 F-1, 46 F-2 and 1 F-3 population revealed monogenic and recessive nature of partial male sterility. To identify single nucleotide polymorphism (SNP) associated with partial male sterility, double-digested restriction site-associated DNA (ddRAD) sequencing of ps1 mutant and its wild type (GPU 28) was performed using Illumina Hi-Seq2000 and shortlisted 69 clusters were functionally annotated in UniProt database. The Cluster 53,954 has annotated MYB-like transcription factor (A0MLT6_ORYSJ) which plays vital role in pollen tube growth, which warrants further validation. Characterization of ps1 mutant in this study demonstrates simplified hybridization in finger millet. This would enable breeders to handle more crosses and frequent hybridization to achieve higher productivity.