Danio meghalayensis is similar to D. dangila, D. assamila, D. catenatus, D. concatenatus, D. sysphigmatus and D. feegradei by the possession of cleithral spot (usually difficult to discern at anterior end of P stripe), complete lateral line, and 14 circumpeduncular scales (vs. 12 or less in other Danio). It is distinguished from those species by the absence (vs. presence) of elongated unbranched ray in pectoral and pelvic fins, rostral barbel not reaching beyond gill cover margin, maxillary barbel not reaching beyond pectoral-fin base (vs. much longer), absence or multiple rows of round or slightly elongate rings on side (vs. presence), branched anal-fin rays 10 1/2-12 1/2 (vs. 13 1/2-16 1/2); from all except D. feegradei by having branched anal-fin count branched dorsal-fin rays 8 1/2 (vs. 9 1/2-10 1/2); different from D. feegradei in presence of horizontal stripes along side, P, P+1 and P-1 stripes distinct, occasionally P and P+1 stripes anastomizing (vs. absence) (Ref. 101154).