Both exams are for engineering entrance. JEE is a national level exam which is conducted to get admission in engineering colleges all over India.
MHT CET exam held by Maharashtra state technical education department. so the college of Maharashtra offers seat under MHT CET and JEE exam.
But one has to appear JEE to get admission in the top colleges of India like IIT'S , NIT'S etc.
If you want admission in top college of Maharashtra
Like COEP,VJTI etc. Can get admssion through both JEE and MHT CET.
It depends on your choice which colleges you prefer, if you want to go in IIT'S you should be giving preference to JEE.

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