Selectivity of five handline fishing hook sizes was determined following Holt’s 1963 model using data that was collected during January to June, 2016. A total of 966 fish specimens comprising of 65 species belonging to 23 families were sampled. Fish abundance was low for large sized hooks while catch rate was higher. Species diversity was higher during the northeast monsoon season and at the study sites of Mpunguti and Nyuli. However, species diversity decreased with increase in hook size. All hook sizes had a higher selection for mature Lethrinus borbonicus while hook size No. 8 selected immature Lethrinus lentjan. Hook sizes No. 9 and 10 selected mature L. lentjan and Lethrinus rubrioperculatus, hook size No. 15 selected immature L. lentjan, L. rubrioperculatus and Aprion virescens, while hook size No. 16 selected immature A. virescens and L. rubrioperculatus. Species similarity was higher for fish caught by hook sizes No. 16 and 15, and No. 8 and 9, while those captured by hook size No. 10 differed from those caught by other hook sizes. The larger hook size No. 8 is recommended for the sustainable exploitation species in the artisanal handline fishery in Shimoni fishing area. Future work needs to consider the effects of bait type and size and the stock status of the fish under exploitation.