Long non-coding RNAs (lncRNAs) play key roles in the regulation of biological processes. Salinity inhibits agricultural productivity. The salinity stress tolerance of barley might play important role to understand the regulatory networks. In this study, we performed quantitative real time-PCR (qPCR) and fluorescence in situ hybridization (FISH) to investigate expression levels of two barley IncRNAs-AK363461 and AK370506-and localizations on four barley genotypes (Hasat, Beysehir 99, Konevi 98 and Tarm 92) under 150mM salt stress conditions during three days germination. Seeds were placed randomly in petri dishes containing filter paper soaked in (a) only H2O (control), (b) 150 mM NaCl for 72 h. RNA extraction were carried out using TriPure (R) reagent from root and shoot samples. Expression analysis demonstrated salinity effected expression levels of AK363461 and AK370506 on shoots and roots during germination. The expression levels of AK363461 for 150mM salt applied groups were altered ranged between (log(2) -0.82 and 0.80) compared controls. However, the expression levels of AK370506 for 150mM salt applied groups were altered ranged between (log(2) -0.64 and 3.16) compared controls. Comparison of AK363461 and AK370506 expression levels, there was statistically significant difference between barley varieties (p<0.05). For FISH application, probes were labelled by tetramethylrhodamine (TRITC) dUTP. The localizations of AK363461 and AK370506 were observed under confocal microscope via FISH on control barley root preparations. Our results is the first direct report to show the relationship between barley IncRNAs and salinity and, also to indicate the localizations of lncRNAs in barley.